https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=Janos EcoliWiki - User contributions [en] 2026-11-03T15:59:45Z User contributions MediaWiki 1.43.11 https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400641 PortEco Microarray Pipeline 2013-07-17T21:34:08Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded (partially)<br /> |<br /> <br /> |<br /> JD: '''4 slides from antisense platform are not loaded'''<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM<br /> <br /> |<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE43659<br /> |<br /> E-GEOD-43659<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD: needs c1-c4<br /> |<br /> virulence/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from Avian Pathogenic Escherichia coli<br /> |<br /> not published<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE48015<br /> |<br /> E-GEOD-48015<br /> |<br /> loaded 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> APEC/transcript profiling<br /> |<br /> 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482<br /> |<br /> not published<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE47418<br /> |<br /> E-GEOD-47418<br /> |<br /> loaded 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> EHEC/co-culture<br /> |<br /> 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression profiling of wt and ydcR mutant strains<br /> |<br /> not published<br /> |<br /> E. coli Genome 2.0 Array<br /> |<br /> GSE48776<br /> |<br /> not yet in AE<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: wait for mage_tab files&lt;br/&gt;<br /> This is part of a superset: GSE48832, which also includes hts dataset GSE48829.<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400640 PortEco Microarray Pipeline 2013-07-17T20:31:29Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded (partially)<br /> |<br /> <br /> |<br /> JD: '''4 slides from antisense platform are not loaded'''<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM<br /> <br /> |<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE43659<br /> |<br /> E-GEOD-43659<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD: needs c1-c4<br /> |<br /> virulence/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from Avian Pathogenic Escherichia coli<br /> |<br /> not published<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE48015<br /> |<br /> E-GEOD-48015<br /> |<br /> in process<br /> |<br /> <br /> |<br /> <br /> |<br /> APEC/transcript profiling<br /> |<br /> 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482<br /> |<br /> not published<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE47418<br /> |<br /> E-GEOD-47418<br /> |<br /> in process<br /> |<br /> <br /> |<br /> <br /> |<br /> EHC/co-culture<br /> |<br /> 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression profiling of wt and ydcR mutant strains<br /> |<br /> not published<br /> |<br /> E. coli Genome 2.0 Array<br /> |<br /> GSE48776<br /> |<br /> not yet in AE<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: wait for mage_tab files&lt;br/&gt;<br /> This is part of a superset: GSE48832, which also includes hts dataset GSE48829.<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400639 PortEco Microarray Pipeline 2013-07-17T20:18:29Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded (partially)<br /> |<br /> <br /> |<br /> JD: '''4 slides from antisense platform are not loaded'''<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM<br /> <br /> |<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE43659<br /> |<br /> E-GEOD-43659<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD: needs c1-c4<br /> |<br /> virulence/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from Avian Pathogenic Escherichia coli<br /> |<br /> not published<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE48015<br /> |<br /> E-GEOD-48015<br /> |<br /> in process<br /> |<br /> <br /> |<br /> <br /> |<br /> APEC/transcript profiling<br /> |<br /> 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482<br /> |<br /> not published<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE47418<br /> |<br /> E-GEOD-47418<br /> |<br /> in process<br /> |<br /> <br /> |<br /> <br /> |<br /> EHC/co-culture<br /> |<br /> 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400638 PortEco Microarray Pipeline 2013-07-17T19:54:40Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> partially loaded<br /> |<br /> <br /> |<br /> JD: 4 slides from antisense platform are not loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM<br /> <br /> |<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE43659<br /> |<br /> E-GEOD-43659<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD: needs c1-c4<br /> |<br /> virulence/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from Avian Pathogenic Escherichia coli<br /> |<br /> not published<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE48015<br /> |<br /> E-GEOD-48015<br /> |<br /> in process<br /> |<br /> <br /> |<br /> <br /> |<br /> APEC/transcript profiling<br /> |<br /> 07/17/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400637 PortEco Microarray Pipeline 2013-07-17T19:10:41Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> partially loaded<br /> |<br /> <br /> |<br /> JD: 4 slides from antisense platform are not loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM<br /> <br /> |<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE43659<br /> |<br /> E-GEOD-43659<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD: needs c1-c4<br /> |<br /> virulence/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400636 PortEco Microarray Pipeline 2013-07-17T00:46:20Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> partially loaded<br /> |<br /> <br /> |<br /> JD: 4 slides from antisense platform are not loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM<br /> <br /> |<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE43659<br /> |<br /> E-GEOD-43659<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: needs c1-c4<br /> |<br /> virulence/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400635 PortEco Microarray Pipeline 2013-07-17T00:09:51Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> partially loaded<br /> |<br /> <br /> |<br /> JD: 4 slides from antisense platform are not loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC) 8624 double deletions of kdpe and cra grown in DMEM<br /> <br /> |<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE43659<br /> |<br /> E-GEOD-43659<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: needs c1-c4<br /> |<br /> <br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400634 PortEco Microarray Pipeline 2013-07-16T23:44:01Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]&lt;br/&gt;<br /> [http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array&lt;br/&gt;<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> partially loaded<br /> |<br /> <br /> |<br /> JD: 4 slides from antisense platform are not loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400633 PortEco Microarray Pipeline 2013-07-16T23:30:51Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]&lt;br/&gt;<br /> [http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3811<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> needs c1-4<br /> |<br /> nucleoid/transcript profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400632 PortEco Microarray Pipeline 2013-07-16T22:48:19Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23536188 pmid]&lt;br/&gt;<br /> [http://www.jbc.org/content/288/19/13789.full jbc]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-3639<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD:<br /> [ idf]&lt;br/&gt;<br /> [ sdrf]<br /> <br /> needs c1 - c4<br /> |<br /> bleach/transcription profiling<br /> |<br /> 07/16/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400631 PortEco Microarray Pipeline 2013-07-16T22:15:23Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> GSE26591<br /> |<br /> E-GEOD-26591<br /> |<br /> loaded (partially, as E-GEOD-26588)<br /> |<br /> <br /> |<br /> JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400630 PortEco Microarray Pipeline 2013-07-16T22:10:25Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> loaded (partially, as E-GEOD-21820)<br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400629 PortEco Microarray Pipeline 2013-07-16T21:58:08Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400628 PortEco Microarray Pipeline 2013-07-16T20:40:23Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Media comparisons/Culturing history<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Media comparisons/H2O2<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> loaded 07/16/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400623 PortEco Microarray Pipeline 2013-07-16T00:50:40Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile acids/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400622 PortEco Microarray Pipeline 2013-07-16T00:15:49Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400621 PortEco Microarray Pipeline 2013-07-15T22:35:01Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> loaded 05/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400620 PortEco Microarray Pipeline 2013-07-15T22:33:07Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> loaded 05/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> loaded 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400619 PortEco Microarray Pipeline 2013-07-15T21:12:49Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug treatment<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400618 PortEco Microarray Pipeline 2013-07-15T21:11:12Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> loaded 07/15/13<br /> |<br /> <br /> |<br /> JD: '''<br /> no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400581 PortEco Microarray Pipeline 2013-07-12T00:30:04Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/transcript profiling<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400580 PortEco Microarray Pipeline 2013-07-12T00:00:37Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type VI secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400579 PortEco Microarray Pipeline 2013-07-11T23:23:45Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> loaded 07/11/13<br /> |<br /> <br /> |<br /> JD '''no cel file available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400564 PortEco Microarray Pipeline 2013-07-11T18:39:48Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein secretion<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400559 PortEco Microarray Pipeline 2013-07-11T00:40:06Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> 07/10/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400557 PortEco Microarray Pipeline 2013-07-10T22:03:52Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biotechnology/Transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400556 PortEco Microarray Pipeline 2013-07-10T21:59:15Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400555 PortEco Microarray Pipeline 2013-07-10T21:55:25Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> loaded 07/10/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> needs c3-4?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400554 PortEco Microarray Pipeline 2013-07-10T20:07:37Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> |<br /> Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/10/13 <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400553 PortEco Microarray Pipeline 2013-07-10T19:19:34Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> <br /> DAS suggestion: Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> loaded 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Persister cells/Stress resistance<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400552 PortEco Microarray Pipeline 2013-07-10T18:14:40Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> <br /> DAS suggestion: Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> 07/08/13<br /> |<br /> <br /> |<br /> JD: '''dataset not in ae, idf/sdrf made from scratch'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Regulation of gene expression<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400551 PortEco Microarray Pipeline 2013-07-10T18:06:49Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> 07/09/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold-shock/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> <br /> DAS suggestion: Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400550 PortEco Microarray Pipeline 2013-07-10T18:00:17Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> 07/08/2013 - DAS<br /> <br /> 07/09/2013 - sent to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> <br /> DAS suggestion: Colony/control or L-form<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> loaded 07/08/13<br /> |<br /> <br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400537 PortEco Microarray Pipeline 2013-07-04T00:38:18Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/Indole<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400536 PortEco Microarray Pipeline 2013-07-03T22:43:40Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> loaded 07/03/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400535 PortEco Microarray Pipeline 2013-07-03T18:22:57Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400532 PortEco Microarray Pipeline 2013-07-03T01:02:46Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> loaded 07/02/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400531 PortEco Microarray Pipeline 2013-07-02T23:08:02Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/(Anaerobic growth/Aerobic Growth)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> |- <br /> |<br /> Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]<br /> |<br /> reloaded 7/02/13<br /> |<br /> yes<br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Strain comparison/cecum<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 07/02/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400530 PortEco Microarray Pipeline 2013-07-01T18:51:37Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400529 PortEco Microarray Pipeline 2013-07-01T18:37:08Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> loaded 7/01/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400524 PortEco Microarray Pipeline 2013-06-29T00:28:40Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> |- <br /> |<br /> changes of global gene expression in E. coli during an oxygen shift<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]<br /> [http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]<br /> GSE1106<br /> GSE1107<br /> |<br /> E-GEOD-1121<br /> |<br /> reloaded 6/28/13<br /> |<br /> yes<br /> |<br /> reloaded due to error during original loading<br /> |<br /> (aerobic/anaerobic)/(mutant/wild-type)<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> 6/28/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400523 PortEco Microarray Pipeline 2013-06-29T00:23:09Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400522 PortEco Microarray Pipeline 2013-06-29T00:18:30Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400521 PortEco Microarray Pipeline 2013-06-29T00:13:13Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400520 PortEco Microarray Pipeline 2013-06-29T00:00:47Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400519 PortEco Microarray Pipeline 2013-06-28T23:57:10Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> loaded 6/28/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400510 PortEco Microarray Pipeline 2013-06-28T00:38:38Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> virulence/Ethanolamine<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> loaded 6/27/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400499 PortEco Microarray Pipeline 2013-06-26T00:55:20Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Ethanolamine/virulence<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> [http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]<br /> [http://dx.plos.org/10.1371/journal.pone.0057860 plosone]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400498 PortEco Microarray Pipeline 2013-06-25T23:54:30Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Ethanolamine/virulence<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 06/25/13 <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos https://ecoliwiki.org/colipedia/index.php?title=PortEco_Microarray_Pipeline&diff=1400497 PortEco Microarray Pipeline 2013-06-25T21:29:18Z <p>Janos: Table edited by Janos via TableEdit</p> <hr /> <div>&lt;protect&gt;&lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;<br /> &lt;!--<br /> ******************************************************************************************<br /> * <br /> * ** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ** <br /> * <br /> ****************************************************************************************** --&gt;<br /> {| border=&quot;2&quot; cellpadding=&quot;4&quot; cellspacing=&quot;0&quot; style=&quot;margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;&quot; id=&quot;K511aabd5a75b9&quot; class=&quot; tableEdit &quot; <br /> |-<br /> !|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started!!geneprofile!!wdk!!zscore!!finished<br /> |- <br /> |<br /> Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array <br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Growth media/adaptation<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Growth media/peroxide<br /> |<br /> 03/20/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt] <br /> <br /> needs c1-c4; new organism? O55:H7<br /> |<br /> Quorum sensing/virulence<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Nitric oxide effect in Escherichia coli O157:H7 EDL933<br /> |<br /> no publication<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]&lt;br/&gt;[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Nitric oxide/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism<br /> |<br /> PMID:23292772 &lt;br/&gt;<br /> [http://jb.asm.org/content/195/6/1167.long jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''no cel files and only norm intensity values'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> |<br /> Stress response/Parkinson's disease<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Fucose sensing regulates bacterial intestinal colonization<br /> |<br /> PMID:23160491<br /> [http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Fucose sensing/colonization<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional responses to the bacteriocin colicin M in Escherichia coli<br /> |<br /> PMID:23421615<br /> [http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> colicins/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli<br /> |<br /> PMID:23222720&lt;br/&gt;<br /> [http://jb.asm.org/content/195/4/807.full jbact]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]<br /> <br /> ready to load?<br /> <br /> |<br /> Two-component systems/transcript profiling<br /> |<br /> 03/24/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)<br /> |<br /> PMID:23071782&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]<br /> |<br /> loaded 06/06/13<br /> <br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Starvation/Phosphate<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence<br /> |<br /> PMID:23163871&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Virulence/Host factors<br /> |<br /> 03/21/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure <br /> |<br /> PMID:23183978&lt;br/&gt;<br /> [http://aem.asm.org/content/79/3/942.long AEM]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]<br /> |<br /> loaded 5/16/13<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Antimicrobial agent/transcription profiling<br /> |<br /> 03/21/13<br /> |<br /> +<br /> |<br /> + Cinnamaldehyde<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression<br /> |<br /> PMID:23472115&lt;br/&gt;<br /> [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]<br /> |<br /> microgravity/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli<br /> |<br /> PMID:22869698&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> ?????/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptional response of E. coli to the presence and absence of bile salts<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> bile salts/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from QdNOs treated Escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]<br /> <br /> needs c4<br /> |<br /> Antimicrobial agent/transcript profiling<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression<br /> |<br /> PMID:23106382&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/24/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> diglutathionylspermidine/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Antitoxin DinJ influences the general stress response through transcript stabilizer CspE<br /> |<br /> PMID:22026739&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]<br /> <br /> needs c3<br /> |<br /> Toxin-antitoxin system/Stress response<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.<br /> |<br /> PMID:22274708&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> biofilm/??????<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7<br /> |<br /> PMID:22589288&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Ethanolamine/virulence<br /> |<br /> 03/22/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-21857<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).<br /> Capture only expression data: E-GEOD-21820<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-TABM-86<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Protein acetylation in prokaryotes increases stress resistance<br /> |<br /> PMID:21703240&lt;br/&gt;<br /> [http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]<br /> <br /> ready to load?<br /> |<br /> Lysine acetylation/stress resistance<br /> |<br /> 03/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40427<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-33212<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-42205<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-40557<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-39439<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35049<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-35822<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41093<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41940<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-41938<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-GEOD-26223<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> E-MTAB-996<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields<br /> |<br /> PMID:22331529<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35371<br /> |<br /> E-GEOD-35371<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]<br /> &lt;br/&gt;<br /> needs c3-c4<br /> |<br /> Transcript profiling/Magnetic field<br /> |<br /> 02/25/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolution of gene expression during long term coexistence in a bacterial evolution experiment<br /> |<br /> PMID:22645336&lt;br/&gt;<br /> [http://www.pnas.org/content/109/24/9487.long PNAS]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30639<br /> |<br /> E-GEOD-30639<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> evolution/chemostat<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.<br /> |<br /> PMID:20886356&lt;br/&gt;<br /> [http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2609<br /> |<br /> loaded 03/25/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]<br /> |<br /> biofilm/urine<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase<br /> |<br /> no publication listed <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE17526<br /> |<br /> E-GEOD-17526<br /> |<br /> loaded 5/14/13<br /> |<br /> 3/30/2013 - DAS<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]<br /> |<br /> Ethanol shock/rpoS<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete on 5/15/13 <br /> |- <br /> |<br /> Expression data from E. coli cells overexpressing GraL for short and long periods of time<br /> |<br /> PMID:20008510<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE15406 &lt;br/&gt;(GSE15404, GSE15405)<br /> |<br /> E-GEOD-15406 &lt;br/&gt;<br /> (E-GEOD-15404, E-GEOD-15405)<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Overexpression/????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate<br /> |<br /> PMID:20501031<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17519<br /> |<br /> E-GEOD-17519<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]&lt;br/&gt;<br /> c1-c4<br /> |<br /> benzoate/??????<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> E. coli response to Antimicrobial Arylamides<br /> |<br /> PMID:21844313<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31140<br /> |<br /> E-GEOD-31140<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 3/17/13 - DAS<br /> <br /> sdrf file at AE didn't have a column for Sample Name<br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]&lt;br/&gt;<br /> needs c3-c4<br /> |<br /> antimicrobial agent/transcription profile<br /> |<br /> 02/26/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock<br /> |<br /> [http://globethesis.com/?t=1100360275976128 globethesis.com]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE17465<br /> |<br /> E-GEOD-17465<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Salt tolerance/Radiation resistance<br /> |<br /> 02/26/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress.<br /> |<br /> PMID:22008207<br /> <br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-623<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> cold treatment/water activity<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.<br /> |<br /> PMID:17145952<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-926<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br /> |<br /> PMID:20444967<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-2298<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]&lt;br/&gt;<br /> <br /> needs c1-c4<br /> |<br /> urine/biofilm<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Impact of cranberry on Escherichia coli cellular surface characteristics.<br /> |<br /> PMID:18957286<br /> <br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12554<br /> |<br /> E-GEOD-12554<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]<br /> <br /> needs c3-c4<br /> |<br /> antibacterial agent/cranberry juice<br /> |<br /> 02/27/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Evolvability and hierarchy in rewired bacterial gene networks.<br /> |<br /> PMID:18421347<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MEXP-732<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt&lt;br/&gt; E-MEXP-732.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]&lt;br/&gt; <br /> needs c1-c4<br /> |<br /> regulatory networks/evolvability<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites<br /> |<br /> no publication<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> GSE34275<br /> |<br /> E-GEOD-34275<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]&lt;br/&gt;<br /> needs c1-c4<br /> |<br /> Growth medium/glycerol<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29440<br /> |<br /> E-GEOD-29440<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data<br /> |<br /> PMID:22018139<br /> <br /> [http://www.amb-express.com/content/1/1/33 www.amb-express.com]<br /> <br /> PMID:22134216<br /> <br /> [http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28412<br /> |<br /> E-GEOD-28412<br /> |<br /> loaded 06/07/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> stress/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture<br /> |<br /> PMID:22018139<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29439<br /> |<br /> E-GEOD-29439<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> recombinant proteins/transcript profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli<br /> |<br /> no publication<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29486<br /> |<br /> E-GEOD-29486<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/recombinant proteins<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.<br /> |<br /> PMID:23090957&lt;br/&gt;<br /> [http://iai.asm.org/content/81/1/80.long IAI]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28399<br /> |<br /> E-GEOD-28399<br /> |<br /> loaded on 5/16/13<br /> |<br /> 4/3/13 - DAS<br /> |<br /> JD: '''missing one cel file'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]<br /> <br /> missing one cel file<br /> |<br /> UPEC/high osmolarity<br /> |<br /> 02/28/13<br /> |<br /> +<br /> |<br /> + OsmolarityUPEC<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Metabolic and transcriptional response to cofactor perturbations in Escherichia coli<br /> |<br /> PMID:20299454&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE20374<br /> |<br /> E-GEOD-20374<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-C4 Completed AMS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> cofactor/transcriptional profiling<br /> |<br /> 02/28/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies<br /> |<br /> PMID:19806199<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE14796<br /> |<br /> E-GEOD-14796<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> L-form/transcription profiling<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of genes induced on nitrate, role of OxyR<br /> |<br /> PMID:22539721&lt;br/&gt;<br /> [http://www.sciencemag.org/content/336/6080/470.long Science]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE24524<br /> |<br /> E-GEOD-24524<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]<br /> <br /> need c3-4<br /> |<br /> anaerobic growth/S-Nitrosylation<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM<br /> |<br /> PMID:22144490<br /> <br /> PMC3264324<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE33895<br /> |<br /> E-GEOD-33895<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]&lt;br/&gt; <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]<br /> <br /> needs c2-c4<br /> |<br /> virulence/His kinase<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa<br /> |<br /> PMID:22101045<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE26931<br /> |<br /> E-GEOD-26931<br /> |<br /> data are loaded in database 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annot from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]<br /> <br /> needs c1-c4<br /> <br /> only loading 4 slides, the ones that are assayed on coli platform<br /> |<br /> mixed culture/transcript profiling<br /> |<br /> 03/01/13<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> + (with GSE26932)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.<br /> |<br /> PMID:21169565&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21551<br /> |<br /> E-GEOD-21551<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03-11-13 - DAS (waiting to hear about strains but OK to load)<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.txt]<br /> <br /> <br /> needs c1-4: DAS added on 03/11/13<br /> <br /> strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used <br /> |<br /> beta-methylthiolation/regulation of gene expression<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol<br /> |<br /> PMID:22936779&lt;br/&gt;<br /> PMID:22936779<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34631<br /> |<br /> E-GEOD-34631<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] &lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> Carbon sources/Enzyme evolution<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans<br /> |<br /> PMID:22792156 &lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30441<br /> |<br /> E-GEOD-30441<br /> |<br /> loaded 5/16/13<br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]&lt;br/&gt;<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]<br /> |<br /> Stress resistance/EtOH<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> + Ethanol-irrE<br /> |<br /> +<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> First insights into the unexplored two-component system YehU/YehT in Escherichia coli.<br /> |<br /> PMID:22685278&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> E-MTAB-984<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> Two-component systems/?????<br /> |<br /> 03/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli<br /> |<br /> PMID:22684885 <br /> [http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35100<br /> |<br /> E-GEOD-35100<br /> |<br /> loaded 03/25/13<br /> re-loaded 04/13/13<br /> |<br /> 03/20/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]<br /> <br /> <br /> |<br /> Chemical effects/Mutant vs Wild-type<br /> |<br /> 03/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine<br /> |<br /> PMID:22101045<br /> <br /> PMC3255741<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE)<br /> |<br /> E-GEOD-26932<br /> |<br /> data loaded 03/19/13<br /> re-loaded 04/15/13<br /> |<br /> used annotation from batch loading<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> use only data on E. coli platform<br /> |<br /> mixed culture/N-acetyl glucosamine<br /> <br /> actual in database: <br /> co-culture/minimal medium<br /> |<br /> 03/04/13<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> + (with GSE26931)<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock<br /> |<br /> PMID:23247721&lt;br/&gt;<br /> [http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE30838<br /> |<br /> E-GEOD-30838<br /> |<br /> completed, 03/18/13<br /> re-loaded 04/15/13<br /> |<br /> 03/14/13 - DAS<br /> <br /> DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt E-GEOD-30838.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]<br /> <br /> needs c1-4: done<br /> <br /> pUC-A1501 described in PMID:19799945<br /> |<br /> glyphosate shock/transcriptional profiling<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Relative expression profiling of ycdC knockout strain secreting HlyA protein<br /> |<br /> PMID:22505047&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE29266<br /> |<br /> E-GEOD-29266<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> biotechnology/protein expression<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis<br /> |<br /> PMID:22210763&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE23417<br /> |<br /> E-GEOD-23417<br /> |<br /> <br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]<br /> <br /> needs c1-c4<br /> |<br /> persistence/Zinc metabolism<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)<br /> |<br /> corresponding author confirmed that data were published in PMID:22196016<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE11303<br /> |<br /> E-GEOD-11303<br /> |<br /> loaded 03/18/13<br /> |<br /> 03/13/2013 - DAS<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]<br /> <br /> needs c3-4: done<br /> |<br /> stress/zinc or Chemical effects/zinc<br /> |<br /> 03/04/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol<br /> |<br /> PMID:22389366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE35797<br /> |<br /> E-GEOD-35797<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Biofilms/drug effects<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.<br /> |<br /> PMID:21398637&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE22207<br /> |<br /> E-GEOD-22207<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> promoter/sigma factor<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC<br /> |<br /> PMID:21255366&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21604<br /> |<br /> E-GEOD-21604<br /> |<br /> loaded 06/24/13<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/mutagenesis<br /> |<br /> 03/04/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.<br /> |<br /> PMID:20855516&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE21893<br /> |<br /> E-GEOD-21893<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> APEC/type Vi secretion system<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type<br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34028<br /> |<br /> E-GEOD-34028<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/14/13<br /> |<br /> 03/12/2013 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt] <br /> <br /> needs c3-4: DAS added 3/12/2013<br /> <br /> |<br /> Persister cells/Mutant vs Wild-type<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin<br /> <br /> |<br /> PMID:22221537&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE31054<br /> |<br /> E-GEOD-31054<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> presistence/???????<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm <br /> |<br /> PMID:22047137&lt;br/&gt;<br /> [http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE28193<br /> |<br /> E-GEOD-28193<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/honey<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli deletion mutant of the nusB gene<br /> |<br /> PMID:21873492<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3335<br /> |<br /> loaded 5/15/13<br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]<br /> <br /> needs c3-4<br /> |<br /> tRNA modificaton/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/16/13 <br /> |- <br /> |<br /> E. coli ygjD gene temperature sensitive mutant incubated at 37 oC<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3334<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.<br /> |<br /> PMID:21873492&lt;br/&gt;<br /> [http://jb.asm.org/content/193/21/6075.full JB]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]<br /> |<br /> <br /> |<br /> E-MEXP-3333<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> tRNA modification/transcript profiling<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages<br /> |<br /> PMID:21221972&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE19953<br /> |<br /> E-GEOD-19953<br /> |<br /> loaded 06/06/13<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> EHEC/biofilm<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.<br /> |<br /> PMID:20005205<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18972<br /> |<br /> E-GEOD-18972<br /> |<br /> loaded 03/19/13<br /> re-loaded 04/13/13<br /> |<br /> 03/11/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> no cel files in ae<br /> |<br /> biofuel/glycerol<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> QseA regulation of virulence factors in EHEC <br /> |<br /> PMID:20444105&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE18118<br /> |<br /> E-GEOD-18118<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br /> <br /> needs c2-4<br /> |<br /> EHEC/virulence<br /> |<br /> 03/05/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development<br /> |<br /> PMID:19060153&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE12701<br /> |<br /> E-GEOD-12701<br /> |<br /> was already loaded as part of publication: &quot;Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae.&quot; together with E-GEOD-11932 <br /> |<br /> c1-4 done, AMS<br /> <br /> 05/15/13 DAS sent idf, sdrf to JD<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br /> <br /> needs c2-4<br /> <br /> modified matrix file Absent-&gt;A, ...<br /> |<br /> biofilm/toxin-antitoxin system<br /> |<br /> 03/05/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)<br /> |<br /> unpublished<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE44273<br /> |<br /> E-GEOD-44273<br /> |<br /> loaded 6/25/13<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> persistence/transcript profiling<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Overexpression of BglJ and LeuO in Escherichia coli K12<br /> |<br /> PMID:22295907&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> GSE34023<br /> |<br /> <br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]<br /> <br /> needs c1-4<br /> <br /> dataset not in ae, idf/sdrf made from scratch<br /> |<br /> ????/??????<br /> |<br /> 03/06/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Expression data from laboratory evolution of Escherichia coli on lactate or glycerol<br /> |<br /> PMID:16204189&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE33147<br /> |<br /> E-GEOD-33147<br /> |<br /> 5/14/13<br /> |<br /> C1-4 done, AMS<br /> <br /> sent idf, sdrf to JD on 5/13/13<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> evolution/carbon source<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete <br /> |- <br /> |<br /> Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.<br /> |<br /> PMID:17112383&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5239<br /> |<br /> E-GEOD-5239<br /> |<br /> 5/27/13<br /> |<br /> 05/26/13<br /> |<br /> JD '''dataset has no cel files and only intensity values!'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]<br /> <br /> |<br /> plasmid/metabolism<br /> |<br /> 03/07/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains<br /> |<br /> PMID:17768236&lt;br/&gt;<br /> [http://mic.sgmjournals.org/content/153/9/2922.long full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)<br /> |<br /> E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)<br /> |<br /> loaded 06/07/13<br /> |<br /> C1-4 done, AMS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> growth phase/fis<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media<br /> |<br /> unpublished<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-TABM-103<br /> |<br /> <br /> |<br /> <br /> |<br /> JD: can't figure out how the experiment was done.<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]<br /> |<br /> <br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli<br /> |<br /> PMID:15705577&lt;br/&gt;<br /> [http://www.jbc.org/content/280/16/15921.long JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2037<br /> |<br /> E-GEOD-2037<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> carbon source/transcript profiling<br /> |<br /> 03/07/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.<br /> |<br /> PMID:17576668&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5818<br /> |<br /> E-GEOD-5818<br /> |<br /> loaded on 5/17/13<br /> |<br /> 03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt E-GEOD-5818.sdrf.txt]<br /> <br /> needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)<br /> <br /> flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD<br /> |<br /> flagellum/regulation<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no - no cel files available<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> Enterobactin is required for biofilm development in reduced-genome Escherichia coli<br /> |<br /> PMID:21980953&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1408<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/22/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]<br /> <br /> needs c1-4<br /> |<br /> biofilm/transcription profiling<br /> <br /> DAS suggests biofilm/Reduced genome<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 05/30/13 <br /> |- <br /> |<br /> Indole cell signaling occurs primarily at low temperatures in Escherichia coli<br /> |<br /> PMID:18528414<br /> |<br /> Ecoli_ASv2 and E_coli_2<br /> |<br /> GSE9923<br /> |<br /> E-GEOD-9923<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]<br /> <br /> needs c2-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Effect of RyhB Small RNA on Global Iron Use in Escherichia coli<br /> |<br /> PMID:16199566&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3105<br /> |<br /> E-GEOD-3105<br /> |<br /> loaded 5/16/13<br /> |<br /> 04/16/13 - DAS<br /> <br /> DAS sent idf, sdrf to JD 05/14/13<br /> |<br /> JD: '''no cel files available'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]<br /> <br /> |<br /> iron/non-coding RNA<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> no: no cel files<br /> |<br /> complete 5/17/13 <br /> |- <br /> |<br /> sigma32 over-expression in E. coli<br /> |<br /> PMID:15757896&lt;br/&gt;<br /> [http://www.jbc.org/content/280/18/17758.long JBC]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE2140<br /> |<br /> E-GEOD-2140<br /> |<br /> loaded 05/31/13<br /> |<br /> 05/26/13 - DAS<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]<br /> <br /> needs c2-4<br /> <br /> no cel files available<br /> |<br /> sigma factor/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (5/31/13) <br /> |- <br /> |<br /> Temporal gene-expression in Escherichia coli K-12 biofilms<br /> |<br /> PMID:17222132&lt;br/&gt;<br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3905<br /> |<br /> E-GEOD-3905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel file available<br /> |<br /> biofilm/transcription profiling<br /> |<br /> 03/08/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation<br /> |<br /> PMID:20809290<br /> <br /> [http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1001<br /> |<br /> loaded 05/30/13<br /> |<br /> 05/27/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/F- phenocopy<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (06/05/13) <br /> |- <br /> |<br /> Indole is an inter-species biofilm signal mediated by SdiA<br /> |<br /> PMID:17511876&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE4562<br /> |<br /> E-GEOD-4562<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> biofilm/indole<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture<br /> |<br /> PMID:17557827&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9203<br /> |<br /> E-GEOD-9203<br /> |<br /> loaded 06/97/13<br /> |<br /> Created C1-C4 AMS<br /> |<br /> JD: '''no cel files available'''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling<br /> |<br /> PMID:16597943&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE3937<br /> |<br /> E-GEOD-3937<br /> |<br /> loaded 5/26/13<br /> |<br /> 05/21/13 - DAS<br /> |<br /> JD: '''no cel files '''<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> - (no cel files)<br /> |<br /> complete (05/30/13) <br /> |- <br /> |<br /> Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)<br /> |<br /> PMID:18309357<br /> <br /> [http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE8706<br /> |<br /> E-GEOD-8706<br /> |<br /> loaded<br /> |<br /> C1-4 done, AMS<br /> <br /> 05/14/13: DAS sent idf/sdrf files to JD<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]<br /> <br /> needs c3-4<br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/11/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (6/05/13) <br /> |- <br /> |<br /> luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling<br /> |<br /> PMID:16321939<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE9587<br /> |<br /> E-GEOD-9587<br /> |<br /> loaded 06/06/13)<br /> |<br /> C1-C4 Complete AMS<br /> |<br /> JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt E-GEOD-9587.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010.<br /> <br /> |<br /> Quorum sensing/(Mutant/wild-type)<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli<br /> |<br /> PMID:18790864&lt;br/&gt;<br /> [http://jb.asm.org/content/190/22/7479.full JB]<br /> |<br /> Ecoli_ASv2<br /> |<br /> <br /> |<br /> E-MEXP-1145<br /> |<br /> loaded 5/15/13<br /> |<br /> 04/03/13 - DAS<br /> |<br /> JD: E-MEXP-953 is part of same pub - already in porteco<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]<br /> |<br /> Biofilm/F plasmid<br /> |<br /> 03/12/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete 5/15/13 <br /> |- <br /> |<br /> YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport<br /> |<br /> PMID:16385049<br /> |<br /> Ecoli_ASv2<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> <br /> conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion <br /> |<br /> Quorum sensing/biofilm<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity<br /> |<br /> PMID:17293424&lt;br/&gt;<br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5904<br /> |<br /> E-GEOD-5904<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> Biofilm/transcription profiling<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803<br /> |<br /> PMID:17521447<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE5905<br /> |<br /> E-GEOD-5905<br /> |<br /> in process<br /> |<br /> <br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]<br /> <br /> needs c3-4<br /> <br /> no cel files available<br /> |<br /> biofuel/biotechnology<br /> |<br /> 03/12/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |- <br /> |<br /> A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS<br /> |<br /> PMID:22941047&lt;br/&gt;<br /> [http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]<br /> |<br /> loaded 03/26/13<br /> re-loaded 04/12/13<br /> <br /> |<br /> 4/4/13 - DAS<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]<br /> <br /> ready to load? - yes (4/4/13 DAS)<br /> |<br /> Toxin-antitoxin system/transcription profiling<br /> |<br /> 03/22/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone - 5/7/13) <br /> |- <br /> |<br /> Evolutionary genome engineering using a restriction–modification system<br /> |<br /> PMID:21785135<br /> <br /> PMC3203608<br /> |<br /> Ecoli_ASv2<br /> |<br /> GSE21869<br /> |<br /> <br /> |<br /> the experimental data are loaded:<br /> <br /> [http://expression.porteco.org/publication.shtml?q=kojima&amp;query=Query&amp;from=0&amp;perpage=500 PortEco Publication]<br /> |<br /> C1-4 done, AMS<br /> |<br /> faked idf/sdrf<br /> |<br /> Evolution/Parental strain<br /> Evolution/Evolved strain<br /> Evolution/Mutant<br /> |<br /> Nov 2012<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/10/13) <br /> |- <br /> |<br /> Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli<br /> |<br /> PMID:19909729<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]<br /> |<br /> persister cells/toxin-antitoxin systems<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (5/14/13) <br /> |- <br /> |<br /> The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli<br /> |<br /> PMID:21292161<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]<br /> |<br /> catabolite repression/non-coding RNA<br /> |<br /> 04/01/13<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> wasn't missing - did not need to reload <br /> |- <br /> |<br /> A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP<br /> |<br /> PMID:16377617<br /> <br /> [http://www.jbc.org/content/281/8/4802.long jbc]<br /> <br /> PMID:17921306<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]<br /> |<br /> A-GEOD-1246.adf.txt <br /> A-GEOD-3051.adf.txt<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]<br /> 2-channel<br /> |<br /> aerobic anaerobic transition/(nitrite/nitrate)<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> The PurR regulon in Escherichia coli K-12 MG1655<br /> |<br /> PMID:21572102<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]<br /> |<br /> purine metabolism/transcript profiling<br /> OR<br /> Chemical effects/wild-type vs mutant<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal<br /> |<br /> PMID:21059164<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]<br /> |<br /> biofilm dispersal/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]<br /> |<br /> PMID:21984790<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]<br /> |<br /> type III secretion system/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 05/08/13) <br /> |- <br /> |<br /> Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]<br /> |<br /> PMID:21930760<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]<br /> |<br /> biofilms/antioxidants<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/7/13) <br /> |- <br /> |<br /> Dynamic omics approach identifies nutrition-mediated microbial interactions.<br /> |<br /> PMID:21058740<br /> <br /> [http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]<br /> <br /> load only coli data<br /> |<br /> co-culture/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD<br /> |<br /> PMID:20105222<br /> <br /> [http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]<br /> |<br /> Affymetrix E. coli Genome 2.0 Array <br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]<br /> |<br /> reload - expression data only<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]<br /> <br /> two platforms - sdrf only contains data for genome 2.0 array<br /> |<br /> toxin antitoxin systems/transcript profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli<br /> |<br /> PMID:21695201<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]<br /> |<br /> Affymetrix GeneChip E.coli Antisense Genome Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]<br /> |<br /> Heat shock/critical high temperature<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (redone 5/8/13) <br /> |- <br /> |<br /> <br /> Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0.<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1872<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine<br /> |<br /> PMID:22753377<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]<br /> |<br /> Affymetrix GeneChip E.coli Genome 2.0 Array<br /> |<br /> <br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> JD<br /> <br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]&lt;br/&gt;<br /> [http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]<br /> |<br /> Asymptomatic Bacteriuria/transcription profiling<br /> |<br /> 04/01/13<br /> |<br /> +<br /> |<br /> =<br /> |<br /> +<br /> |<br /> complete (redone 5/9/13) <br /> |- <br /> |<br /> <br /> Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC<br /> |<br /> PMID:19240136<br /> <br /> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]<br /> |<br /> A-MEXP-1444<br /> |<br /> <br /> |<br /> E-MEXP-1877<br /> |<br /> reload<br /> |<br /> yes<br /> |<br /> <br /> |<br /> blue-light response/two-component system<br /> |<br /> <br /> |<br /> +<br /> |<br /> +<br /> |<br /> +<br /> |<br /> complete (reloaded 5/14/13) <br /> |- <br /> |<br /> Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110<br /> |<br /> PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]<br /> |<br /> Affymetrix E. coli Antisense Genome Array<br /> |<br /> [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]<br /> |<br /> [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]<br /> |<br /> reloaded 6/25/13<br /> |<br /> <br /> |<br /> redoing this data set because there was a problem with the original loading<br /> |<br /> Stress/pH (external)<br /> |<br /> 06/21/2013<br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> |<br /> <br /> <br /> |- class=&quot;tableEdit_footer&quot; <br /> |&lt;span class=&quot;tableEdit_editLink plainlinks&quot;&gt;[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&amp;id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&amp;page=182907&amp;pagename={{FULLPAGENAMEE}}&amp;type=0&amp;template= edit table]&lt;/span&gt; || || || || || || || || || || || || ||<br /> |}<br /> &lt;!--box uid=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9--&gt;&lt;/protect&gt;<br /> <br /> <br /> <br /> <br /> &lt;references/&gt; <br /> {{RefHelp}}<br /> <br /> [[Category:PortEco]] [[Category:Expression data]]</div> Janos