PortEco Microarray Pipeline: Difference between revisions
Table edited by Janos via TableEdit |
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[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779] | [http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779] | ||
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loaded 03/26/13 | |||
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needs verification | |||
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JD | JD | ||
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ready to load? | ready to load? | ||
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Toxin-antitoxin system/transcription profiling | |||
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03/22/13 | 03/22/13 | ||
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+ | |||
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needs verification | |||
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Revision as of 22:02, 26 March 2013
| Title/Dataset Description | Reference | Platform | GEO Accession | ArrayExpress Accession | Data loaded | Curation completed | Notes | category/subcat | date started | geneprofile | wdk | zscore | finished |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
in process |
JD E-MEXP-3800.idf.txt needs c1-4 |
Growth media/adaptation |
03/20/13 |
|||||||
|
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 |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
in process |
JD E-MEXP-3799.idf.txt needs c1-4 |
Growth media/peroxide |
03/20/13 |
|||||||
|
Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor |
no publication |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-43325.idf.txt needs c1-c4; new organism? O55:H7 |
Quorum sensing/virulence |
03/21/13 |
|||||||
|
Nitric oxide effect in Escherichia coli O157:H7 EDL933 |
no publication |
in process |
JD E-GEOD-29076.idf.txt needs c1-4 |
Nitric oxide/transcription profiling |
03/21/13 |
||||||||
|
Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism |
Affymetrix E. coli Genome 2.0 Array |
[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020 |
in process |
JD E-GEOD-42702.idf.txt needs c1-4 no cel files |
Stress response/Parkinson's disease |
03/21/13 |
|||||||
|
Fucose sensing regulates bacterial intestinal colonization |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-34991.idf.txt needs c1-4 |
Fucose sensing/colonization |
03/21/13 |
||||||||
|
Global transcriptional responses to the bacteriocin colicin M in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-37026.idf.txt needs c1-4 |
colicins/transcription profiling |
03/21/13 |
||||||||
|
Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
in process |
JD E-MTAB-1347.idf.txt ready to load? |
Two-component systems/transcript profiling |
03/24/13 |
||||||||
|
Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data) |
Affymetrix E. coli Genome 2.0 Array |
[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820' |
in process |
JD E-GEOD-21820.idf.txt needs c1-4 |
Starvation/Phosphate |
03/21/13 |
|||||||
|
Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-22285.idf.txt needs c1-4 |
Virulence/Host factors |
03/21/13 |
||||||||
|
Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-40693.idf.txt needs c1-4 |
Antimicrobial agent/transcription profiling |
03/21/13 |
||||||||
|
Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-40648.idf.txt ready to load? |
microgravity/transcript profiling |
03/22/13 |
||||||||
|
Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-21652.idf.txt needs c3-4 |
?????/?????? |
03/22/13 |
||||||||
|
Global transcriptional response of E. coli to the presence and absence of bile salts |
no publication |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-20380.idf.txt ready to load? |
bile salts/transcript profiling |
03/22/13 |
|||||||
|
Expression data from QdNOs treated Escherichia coli |
no publication |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-39607.idf.txt needs c4 |
Antimicrobial agent/transcript profiling |
03/22/13 |
|||||||
|
Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-30679.idf.txt needs c3-4 |
diglutathionylspermidine/transcription profiling |
03/22/13 |
||||||||
|
Antitoxin DinJ influences the general stress response through transcript stabilizer CspE |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-30692.idf.txt needs c3 |
antitoxin/transcript profiling |
03/22/13 |
||||||||
|
Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation. |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-30424.idf.txt ready to load? |
biofilm/?????? |
03/22/13 |
||||||||
|
Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7 |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-34046.idf.txt ready to load? |
Ethanolamine/virulence |
03/22/13 |
||||||||
|
E-GEOD-21857 |
JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen). Capture only expression data: E-GEOD-21820 |
||||||||||||
|
E-TABM-86 |
|||||||||||||
|
Protein acetylation in prokaryotes increases stress resistance |
Affymetrix E. coli Genome 2.0 Array |
in process |
JD E-GEOD-29803.idf.txt ready to load? |
Lysine acetylation/stress resistance |
03/25/13 |
||||||||
|
E-GEOD-40427 |
|||||||||||||
|
E-GEOD-33212 |
|||||||||||||
|
E-GEOD-42205 |
|||||||||||||
|
E-GEOD-40557 |
|||||||||||||
|
E-GEOD-39439 |
|||||||||||||
|
E-GEOD-35049 |
|||||||||||||
|
E-GEOD-35822 |
|||||||||||||
|
E-GEOD-41093 |
|||||||||||||
|
E-GEOD-41940 |
|||||||||||||
|
E-GEOD-41938 |
|||||||||||||
|
E-GEOD-26223 |
|||||||||||||
|
E-MTAB-996 |
|||||||||||||
|
Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields |
Affymetrix E. coli Genome 2.0 Array |
GSE35371 |
E-GEOD-35371 |
in process |
JD |
Transcript profiling/Magnetic field |
02/25/13 |
||||||
|
Evolution of gene expression during long term coexistence in a bacterial evolution experiment |
http://www.ncbi.nlm.nih.gov/pubmed/22645336 |
Affymetrix E. coli Genome 2.0 Array |
GSE30639 |
E-GEOD-30639 |
in process |
JD |
evolution/chemostat |
02/26/13 |
|||||
|
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. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-2609 |
loaded 03/25/13 |
03/20/13 - DAS |
biofilm/urine |
02/26/13 |
+ |
+ |
+ |
done | |||
|
Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE17526 |
E-GEOD-17526 |
in process |
ETOH shock/rpoS |
02/26/13 |
||||||
|
Expression data from E. coli cells overexpressing GraL for short and long periods of time |
Affymetrix E. coli Genome 2.0 Array |
GSE15406 |
E-GEOD-15406 |
in process |
JD |
Overexpression/???? |
02/26/13 |
||||||
|
Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate |
Affymetrix E. coli Genome 2.0 Array |
GSE17519 |
E-GEOD-17519 |
in process |
JD |
benzoate/?????? |
02/26/13 |
||||||
|
E. coli response to Antimicrobial Arylamides |
Affymetrix E. coli Genome 2.0 Array |
GSE31140 |
E-GEOD-31140 |
loaded 03/19/13 |
3/17/13 - DAS sdrf file at AE didn't have a column for Sample Name |
JD needs c3-c4 |
antimicrobial agent/transcription profile |
02/26/13 |
+ |
+ |
+ |
done | |
|
Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock |
Affymetrix E. coli Genome 2.0 Array |
GSE17465 |
E-GEOD-17465 |
in process |
JD |
Salt tolerance/Radiation resistance |
02/26/13 |
||||||
|
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. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MTAB-623 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt needs c3-c4 |
cold treatment/water activity |
02/27/13 |
|||||||
|
Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-926 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt needs c2-4 |
urine/biofilm |
02/27/13 |
|||||||
|
Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-2298 |
in process |
JD
http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt needs c1-c4 |
urine/biofilm |
02/27/13 |
|||||||
|
Impact of cranberry on Escherichia coli cellular surface characteristics. |
Affymetrix E. coli Genome 2.0 Array |
GSE12554 |
E-GEOD-12554 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt needs c3-c4 |
antibacterial agent/cranberry juice |
02/27/13 |
||||||
|
Evolvability and hierarchy in rewired bacterial gene networks. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-732 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt |
regulatory networks/evolvability |
02/28/13 |
|||||||
|
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 |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE34275 |
E-GEOD-34275 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt needs c1-c4 |
Growth medium/glycerol |
02/28/13 |
|||||
|
Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
GSE29440 |
E-GEOD-29440 |
in process |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 |
||||||
|
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 |
http://www.amb-express.com/content/1/1/33 http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g |
Affymetrix E. coli Genome 2.0 Array |
GSE28412 |
E-GEOD-28412 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 |
|||||
|
Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture |
Affymetrix E. coli Genome 2.0 Array |
GSE29439 |
E-GEOD-29439 |
in process |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 |
||||||
|
Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli |
no publication |
Affymetrix E. coli Genome 2.0 Array |
GSE29486 |
E-GEOD-29486 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 |
|||||
|
Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea. |
http://www.ncbi.nlm.nih.gov/pubmed/23090957 |
Affymetrix E. coli Genome 2.0 Array |
GSE28399 |
E-GEOD-28399 |
in process |
JD E-GEOD-28399.idf.txt needs c3-c4 missing one cel file |
UPEC/high osmolarity |
02/28/13 |
|||||
|
Metabolic and transcriptional response to cofactor perturbations in Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/20299454 |
Affymetrix E. coli Genome 2.0 Array |
GSE20374 |
E-GEOD-20374 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt needs c1-c4 |
cofactor/transcriptional profiling |
02/28/13 |
|||||
|
Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies |
Affymetrix E. coli Genome 2.0 Array |
GSE14796 |
E-GEOD-14796 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt needs c3-4 |
L-form/transcription profiling |
03/01/13 |
||||||
|
Identification of genes induced on nitrate, role of OxyR |
http://www.ncbi.nlm.nih.gov/pubmed/22539721 |
Affymetrix E. coli Genome 2.0 Array |
GSE24524 |
E-GEOD-24524 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt need c3-4 |
anaerobic growth/S-Nitrosylation |
03/01/13 |
|||||
|
Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM |
PMC3264324 |
Affymetrix E. coli Genome 2.0 Array |
GSE33895 |
E-GEOD-33895 |
in process |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt needs c2-c4 |
virulence/His kinase |
03/01/13 |
|||||
|
Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa |
Affymetrix E. coli Genome 2.0 Array |
GSE26931 |
E-GEOD-26931 |
data are loaded in database 03/19/13 |
used annot from batch loading |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt needs c1-c4 only loading 4 slides, the ones that are assayed on coli platform |
mixed culture/transcription profiling |
03/01/13 |
+ (with GSE26932) |
+ (with GSE26932) |
+ (with GSE26932) |
done | |
|
A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. |
http://www.ncbi.nlm.nih.gov/pubmed/21169565 |
Affymetrix E. coli Genome 2.0 Array |
GSE21551 |
E-GEOD-21551 |
loaded 03/19/13 |
03-11-13 - DAS (waiting to hear about strains but OK to load) |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt
needs c1-4: DAS added on 03/11/13 strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used |
beta-methylthiolation/regulation |
03/01/13 |
+ |
+ |
+ |
done |
|
Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol |
http://www.ncbi.nlm.nih.gov/pubmed/22936779 |
Affymetrix E. coli Genome 2.0 Array |
GSE34631 |
E-GEOD-34631 |
loaded 03/19/13 |
03/12/13 - DAS |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt needs c3-4: done |
Carbon sources/Enzyme evolution |
03/01/13 |
+ |
+ |
+ |
done |
|
Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans |
http://www.ncbi.nlm.nih.gov/pubmed/?term=22792156 |
Affymetrix E. coli Genome 2.0 Array |
GSE30441 |
E-GEOD-30441 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt needs c1-4 |
Stress resistance/EtOH |
03/01/13 |
|||||
|
First insights into the unexplored two-component system YehU/YehT in Escherichia coli. |
http://www.ncbi.nlm.nih.gov/pubmed/22685278 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MTAB-984 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt needs c1-4 |
Two-component systems/????? |
03/01/13 |
||||||
|
Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli |
Affymetrix E. coli Genome 2.0 Array |
GSE35100 |
E-GEOD-35100 |
loaded 03/25/13 |
03/20/13 - DAS |
JD
E-GEOD-35100.idf.txt
|
Chemical effects/Mutant vs Wild-type |
03/01/13 |
+ |
+ |
+ |
done | |
|
Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine |
PMC3255741 |
Affymetrix E. coli Genome 2.0 Array |
GSE26932 |
E-GEOD-26932 |
data loaded 03/19/13 http://expression.porteco.org/publication.shtml?q=zere&query=Query&from=0&perpage=500 |
used annotation from batch loading |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt needs c3-4 use only data on E. coli platform |
mixed culture/N-acetyl glucosamine actual in database: co-culture/minimal medium |
03/04/13 |
+ (with GSE26931) |
+ (with GSE26931) |
+ (with GSE26931) |
done |
|
Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock |
http://www.ncbi.nlm.nih.gov/pubmed/23247721 |
Affymetrix E. coli Genome 2.0 Array |
GSE30838 |
E-GEOD-30838 |
completed, 03/18/13 |
03/14/13 - DAS DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is. |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt needs c1-4: done pUC-A1501 described in PMID:19799945[15] |
glyphosate shock/transcriptional profiling |
03/04/13 |
+ |
+ |
+ |
done |
|
Relative expression profiling of ycdC knockout strain secreting HlyA protein |
http://www.ncbi.nlm.nih.gov/pubmed/22505047 |
Affymetrix E. coli Genome 2.0 Array |
GSE29266 |
E-GEOD-29266 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt needs c1-c4 |
biotechnology/protein expression |
03/04/13 |
|||||
|
Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis |
http://www.ncbi.nlm.nih.gov/pubmed/22210763 |
Affymetrix E. coli Genome 2.0 Array |
GSE23417 |
E-GEOD-23417 |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt needs c1-c4 |
persistence/Zinc metabolism |
03/04/13 |
||||||
|
Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine) |
corresponding author confirmed that data were published in PMID:22196016[16] |
Affymetrix E. coli Genome 2.0 Array |
GSE11303 |
E-GEOD-11303 |
loaded 03/18/13 |
03/13/2013 - DAS |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt needs c3-4: done |
stress/zinc or Chemical effects/zinc |
03/04/13 |
+ |
+ |
+ |
done |
|
Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol |
http://www.ncbi.nlm.nih.gov/pubmed/22389366 |
Affymetrix E. coli Genome 2.0 Array |
GSE35797 |
E-GEOD-35797 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt needs c3-4 |
Biofilms/drug effects |
03/04/13 |
|||||
|
Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase. |
http://www.ncbi.nlm.nih.gov/pubmed/21398637 |
Affymetrix E. coli Genome 2.0 Array |
GSE22207 |
E-GEOD-22207 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt needs c3-4 |
promoter/sigma factor |
03/04/13 |
|||||
|
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 |
http://www.ncbi.nlm.nih.gov/pubmed/21255366 |
Affymetrix E. coli Genome 2.0 Array |
GSE21604 |
E-GEOD-21604 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt<r/> http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt needs c2-4 no raw data files in ae |
biofilm/mutagenesis |
03/04/13 |
|||||
|
The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain. |
http://www.ncbi.nlm.nih.gov/pubmed/20855516 |
Affymetrix E. coli Genome 2.0 Array |
GSE21893 |
E-GEOD-21893 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt needs c3-4 |
APEC/type Vi secretion system |
03/05/13 |
|||||
|
BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type |
http://www.ncbi.nlm.nih.gov/pubmed/22221537 |
Affymetrix E. coli Genome 2.0 Array |
GSE34028 |
E-GEOD-34028 |
loaded 03/19/13 |
03/12/2013 - DAS |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt needs c3-4: DAS added 3/12/2013
|
Persister cells/Mutant vs Wild-type |
03/05/13 |
+ |
+ |
+ |
done |
|
Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin |
http://www.ncbi.nlm.nih.gov/pubmed/22221537 |
Affymetrix E. coli Genome 2.0 Array |
GSE31054 |
E-GEOD-31054 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt needs c3-4 |
presistence/??????? |
03/05/13 |
|||||
|
Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm |
http://www.ncbi.nlm.nih.gov/pubmed/22047137 |
Affymetrix E. coli Genome 2.0 Array |
GSE28193 |
E-GEOD-28193 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt needs c3-4 |
biofilm/honey |
03/05/13 |
|||||
|
The E. coli deletion mutant of the nusB gene |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3335 |
in process |
JD
http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt needs c3-4 |
tRNA modificaton/transcript profiling |
03/05/13 |
|||||||
|
E. coli ygjD gene temperature sensitive mutant incubated at 37 oC |
www.ncbi.nlm.nih.gov/pubmed/21873492 |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3334 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt needs c1-4 |
tRNA modification/transcript profiling |
03/05/13 |
||||||
|
The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C. |
www.ncbi.nlm.nih.gov/pubmed/21873492 |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3333 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt needs c2-4 |
tRNA modification/transcript profiling |
03/05/13 |
||||||
|
Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages |
http://www.ncbi.nlm.nih.gov/pubmed/21221972 |
Affymetrix E. coli Genome 2.0 Array |
GSE19953 |
E-GEOD-19953 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt needs c3-4 |
EHEC/biofilm |
03/05/13 |
|||||
|
An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol. |
Affymetrix E. coli Genome 2.0 Array |
GSE18972 |
E-GEOD-18972 |
loaded 03/19/13 |
03/11/13 - DAS |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt needs c1-4 no cel files in ae |
biofuel/glycerol |
03/05/13 |
+ |
+ |
- (no cel files) |
done (but no zscores) | |
|
QseA regulation of virulence factors in EHEC |
http://www.ncbi.nlm.nih.gov/pubmed/20444105 |
Affymetrix E. coli Genome 2.0 Array |
GSE18118 |
E-GEOD-18118 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt needs c2-4 |
EHEC/virulence |
03/05/13 |
|||||
|
Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development |
http://www.ncbi.nlm.nih.gov/pubmed/19060153 |
Affymetrix E. coli Genome 2.0 Array |
GSE12701 |
E-GEOD-12701 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt needs c2-4 modified matrix file Absent->A, ... |
biofilm/toxin-antitoxin system |
03/05/13 |
|||||
|
Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates) |
unpublished |
Affymetrix E. coli Genome 2.0 Array |
GSE44273 |
E-GEOD-44273 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt needs c1-4 |
persistence/transcript profiling |
03/06/13 |
|||||
|
Overexpression of BglJ and LeuO in Escherichia coli K12 |
http://www.ncbi.nlm.nih.gov/pubmed/22295907 |
Affymetrix E. coli Genome 2.0 Array |
GSE34023 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt needs c1-4 dataset not in ae, idf/sdrf made from scratch |
????/?????? |
03/06/13 |
||||||
|
Expression data from laboratory evolution of Escherichia coli on lactate or glycerol |
http://www.ncbi.nlm.nih.gov/pubmed/16204189 |
Ecoli_ASv2 |
GSE33147 |
E-GEOD-33147 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt needs c3-4 |
evolution/carbon source |
03/07/13 |
|||||
|
Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. |
http://www.ncbi.nlm.nih.gov/pubmed/17112383 |
Ecoli_ASv2 |
GSE5239 |
E-GEOD-5239 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt needs c1-4 dataset has no cel files |
plasmid/metabolism |
03/07/13 |
|||||
|
Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains |
http://www.ncbi.nlm.nih.gov/pubmed/17768236 |
Ecoli_ASv2 |
GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt) |
E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt) |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt needs c1-4 |
????/transcription profiling |
03/07/13 |
|||||
|
Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media |
unpublished |
Ecoli_ASv2 |
E-TABM-103 |
JD: can't figure out how the experiment was done. http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt |
03/07/13 |
||||||||
|
Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/15705577 |
Ecoli_ASv2 |
GSE2037 |
E-GEOD-2037 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt no cel files available |
carbon source/transcript profiling |
03/07/13 |
|||||
|
Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli. |
http://www.ncbi.nlm.nih.gov/pubmed/17576668 |
Ecoli_ASv2 |
GSE5818 |
E-GEOD-5818 |
in process |
03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load) |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt 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) no cel files available 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 |
flagellum/regulation |
03/08/13 |
||||
|
Enterobactin is required for biofilm development in reduced-genome Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/21980953 |
Ecoli_ASv2 |
E-MEXP-1408 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt needs c1-4 |
biofilm/transcription profiling |
03/08/13 |
||||||
|
Indole cell signaling occurs primarily at low temperatures in Escherichia coli |
Ecoli_ASv2 and E_coli_2 |
GSE9923 |
E-GEOD-9923 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt needs c2-4 |
biofilm/indole |
03/08/13 |
||||||
|
Effect of RyhB Small RNA on Global Iron Use in Escherichia coli |
http://www.ncbi.nlm.nih.gov/pubmed/16199566 |
Ecoli_ASv2 |
GSE3105 |
E-GEOD-3105 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt needs c2-4 no cel files available |
iron/non-coding RNA |
03/08/13 |
|||||
|
sigma32 over-expression in E. coli |
http://www.ncbi.nlm.nih.gov/pubmed/15757896 |
Ecoli_ASv2 |
GSE2140 |
E-GEOD-2140 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt needs c2-4 no cel files available |
sigma factor/transcription profiling |
03/08/13 |
|||||
|
Temporal gene-expression in Escherichia coli K-12 biofilms |
http://www.ncbi.nlm.nih.gov/pubmed/17222132 |
Ecoli_ASv2 |
GSE3905 |
E-GEOD-3905 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt needs c3-4 ne cel file available |
biofilm/transcription profiling |
03/08/13 |
|||||
|
Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation |
http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt |
Ecoli_ASv2 |
E-MEXP-1001 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt needs c3-4 |
biofilm/F- phenocopy |
03/11/13 |
||||||
|
Indole is an inter-species biofilm signal mediated by SdiA |
http://www.ncbi.nlm.nih.gov/pubmed/17511876 |
Ecoli_ASv2 |
GSE4562 |
E-GEOD-4562 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt needs c3-4 |
biofilm/indole |
03/11/13 |
|||||
|
Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture |
http://www.ncbi.nlm.nih.gov/pubmed/17557827 |
Ecoli_ASv2 |
GSE9203 |
E-GEOD-9203 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt needs c3-4 no cel files available |
Quorum sensing/biofilm |
03/11/13 |
|||||
|
YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling |
http://www.ncbi.nlm.nih.gov/pubmed/16597943 |
Ecoli_ASv2 |
GSE3937 |
E-GEOD-3937 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt needs c3-4 no cel files |
Quorum sensing/biofilm |
03/11/13 |
|||||
|
Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA) |
http://www.ncbi.nlm.nih.gov/pubmed/18309357 |
Ecoli_ASv2 |
GSE8706 |
E-GEOD-8706 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt needs c3-4 no cel files |
Quorum sensing/biofilm |
03/11/13 |
|||||
|
luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling |
Ecoli_ASv2 |
GSE9587 |
E-GEOD-9587 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt needs c3-4 paper talks about expts in low/high glucose, but only low glucose data are in the set. |
Quorum sensing/transcription profiling |
03/12/13 |
||||||
|
Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli |
http://www.ncbi.nlm.nih.gov/pubmed/18790864 |
Ecoli_ASv2 |
E-MEXP-1145 |
in process |
JD: E-MEXP-953 is part of same pub - already in porteco
http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt |
Biofilm/F plasmid |
03/12/13 |
||||||
|
YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport |
Ecoli_ASv2 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt needs c3-4 no cel files available conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion |
Quorum sensing/biofilm |
03/12/13 |
||||||||
|
YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity |
http://www.ncbi.nlm.nih.gov/pubmed/17293424 |
Ecoli_ASv2 |
GSE5904 |
E-GEOD-5904 |
in process |
JD http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt needs c3-4 no cel files available |
Biofilm/transcription profiling |
03/12/13 |
|||||
|
Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803 |
Ecoli_ASv2 |
GSE5905 |
E-GEOD-5905 |
in process |
JD
http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt needs c3-4 ne cel files available |
biofuel/biotechnology |
03/12/13 |
||||||
|
A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS |
Affymetrix E. coli Genome 2.0 Array |
loaded 03/26/13 |
needs verification |
JD E-GEOD-36779.idf.txt ready to load? |
Toxin-antitoxin system/transcription profiling |
03/22/13 |
+ |
+ |
+ |
needs verification | |||
|
Evolutionary genome engineering using a restriction–modification system |
PMC3203608 |
Ecoli_ASv2 |
GSE21869 |
the experimental data are loaded: http://expression.porteco.org/publication.shtml?q=kojima&query=Query&from=0&perpage=500 |
no idf/sdrf |
Evolution/Parental strain Evolution/Evolved strain Evolution/Mutant |
Nov 2012 |
||||||
|
Expression profiles of evolved clones isolated at various stages during adaptive experimental evolution of E. coli |
PMC3203608 |
Ecoli_ASv2 |
GSE21869 |
loaded 11/13/12 |
no idf/sdrf no expt factors |
loaded as batch |
Evolution/Evolved strain or Mutant |
+ |
- (no idf/sdrf) |
- (no idf/sdrf) |
| ||
| edit table |
- ↑ Huwiler, SG et al. (2012) Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields. Bioelectromagnetics 33 488-96 PubMed
- ↑ Potrykus, K et al. (2010) Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. Nucleic Acids Res. 38 1636-51 PubMed
- ↑ Critzer, FJ et al. (2010) Increased transcription of the phosphate-specific transport system of Escherichia coli O157:H7 after exposure to sodium benzoate. J. Food Prot. 73 819-24 PubMed
- ↑ Mensa, B et al. (2011) Antibacterial mechanism of action of arylamide foldamers. Antimicrob. Agents Chemother. 55 5043-53 PubMed
- ↑ Kocharunchitt, C et al. (2012) 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. Mol. Cell Proteomics 11 M111.009019 PubMed
- ↑ Hancock, V & Klemm, P (2007) Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine. Infect. Immun. 75 966-76 PubMed
- ↑ Watts, RE et al. (2010) Escherichia coli isolates causing asymptomatic bacteriuria in catheterized and noncatheterized individuals possess similar virulence properties. J. Clin. Microbiol. 48 2449-58 PubMed
- ↑ Johnson, BJ et al. (2008) Impact of cranberry on Escherichia coli cellular surface characteristics. Biochem. Biophys. Res. Commun. 377 992-4 PubMed
- ↑ Isalan, M et al. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452 840-5 PubMed
- ↑ 10.0 10.1 10.2 Sharma, AK et al. (2011) Comparative transcriptomic profile analysis of fed-batch cultures expressing different recombinant proteins in Escherichia coli. AMB Express 1 33 PubMed
- ↑ Singh, AB et al. (2012) 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. Mol Biosyst 8 615-28 PubMed
- ↑ Glover, WA et al. (2009) Insights into the molecular basis of L-form formation and survival in Escherichia coli. PLoS ONE 4 e7316 PubMed
- ↑ Njoroge, J & Sperandio, V (2012) Enterohemorrhagic Escherichia coli virulence regulation by two bacterial adrenergic kinases, QseC and QseE. Infect. Immun. 80 688-703 PubMed
- ↑ 14.0 14.1 Chu, W et al. (2012) Indole production promotes Escherichia coli mixed-culture growth with Pseudomonas aeruginosa by inhibiting quorum signaling. Appl. Environ. Microbiol. 78 411-9 PubMed
- ↑ Li, L et al. (2009) A novel RPMXR motif among class II 5-enolpyruvylshikimate-3-phosphate synthases is required for enzymatic activity and glyphosate resistance. J. Biotechnol. 144 330-6 PubMed
- ↑ Hensley, MP et al. (2012) Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli. J. Inorg. Biochem. 111 164-72 PubMed
- ↑ Hashimoto, C et al. (2011) Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli. J. Bacteriol. 193 6075-9 PubMed
- ↑ Hu, H & Wood, TK (2010) An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol. Biochem. Biophys. Res. Commun. 391 1033-8 PubMed
- ↑ Lee, J et al. (2008) Indole cell signaling occurs primarily at low temperatures in Escherichia coli. ISME J 2 1007-23 PubMed
- ↑ Wang, L et al. (2005) luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling. J. Bacteriol. 187 8350-60 PubMed
- ↑ Herzberg, M et al. (2006) YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. J. Bacteriol. 188 587-98 PubMed
- ↑ Maeda, T et al. (2007) Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803. BMC Biotechnol. 7 25 PubMed
- ↑ 23.0 23.1 Asakura, Y et al. (2011) Evolutionary genome engineering using a restriction-modification system. Nucleic Acids Res. 39 9034-46 PubMed
See Help:References for how to manage references in EcoliWiki.