PortEco Microarray Pipeline
| Title/Dataset Description | Reference | Platform | GEO Accession | ArrayExpress Accession | Data loaded | Curation completed | Notes | category/subcat | date started |
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Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions |
E-MEXP-3800 |
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E-MEXP-3799 |
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E-GEOD-43325 |
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E-GEOD-29076 |
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E-GEOD-42702 |
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E-GEOD-34991 |
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E-GEOD-37026 |
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E-MTAB-1347 |
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E-GEOD-21820 |
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E-GEOD-22285 |
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E-GEOD-40693 |
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E-GEOD-40648 |
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E-GEOD-21652 |
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E-GEOD-36779 |
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E-GEOD-20380 |
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E-GEOD-39607 |
JD: skipped it |
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E-GEOD-30679 |
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E-GEOD-30692 |
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E-GEOD-30424 |
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E-GEOD-34046 |
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E-GEOD-21857 |
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E-TABM-86 |
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E-GEOD-29803 |
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E-GEOD-40427 |
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E-GEOD-33212 |
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E-GEOD-42205 |
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E-GEOD-40557 |
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E-GEOD-39439 |
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E-GEOD-35049 |
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E-GEOD-35822 |
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E-GEOD-41093 |
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E-GEOD-41940 |
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E-GEOD-41938 |
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E-GEOD-26223 |
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E-MTAB-996 |
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Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields |
http://www.ncbi.nlm.nih.gov/pubmed/22331529 |
Affymetrix E. coli Genome 2.0 Array |
GSE35371 |
E-GEOD-35371 |
in process |
JD |
Transcript profiling/Magnetic field |
02/25/13 | |
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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 | |
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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. |
http://www.ncbi.nlm.nih.gov/pubmed/20886356 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-2609 |
in process |
JD |
biofilm/urine |
02/26/13 | ||
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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 |
JD |
ETOH shock/rpoS |
02/26/13 | |
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Expression data from E. coli cells overexpressing GraL for short and long periods of time |
http://www.ncbi.nlm.nih.gov/pubmed/20008510 |
Affymetrix E. coli Genome 2.0 Array |
GSE15406 |
E-GEOD-15406 |
in process |
JD |
Overexpression/???? |
02/26/13 | |
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Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate |
http://www.ncbi.nlm.nih.gov/pubmed/20501031 |
Affymetrix E. coli Genome 2.0 Array |
GSE17519 |
E-GEOD-17519 |
in process |
JD |
benzoate/?????? |
02/26/13 | |
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E.coli response to Antimicrobial Arylamides |
http://www.ncbi.nlm.nih.gov/pubmed/21844313 |
Affymetrix E. coli Genome 2.0 Array |
GSE31140 |
E-GEOD-31140 |
in process |
JD |
antimicrobial agent/transcription profile |
02/26/13 | |
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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 | ||
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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. |
http://www.ncbi.nlm.nih.gov/pubmed/22008207 |
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 | ||
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Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine. |
http://www.ncbi.nlm.nih.gov/pubmed/?term=17145952 |
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 | ||
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Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine. |
http://www.ncbi.nlm.nih.gov/pubmed/20444967 |
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 | ||
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Impact of cranberry on Escherichia coli cellular surface characteristics. |
http://www.ncbi.nlm.nih.gov/pubmed/18957286 |
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 needs c3-c4 |
antibacterial agent/cranberry juice |
02/27/13 | |
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Evolvability and hierarchy in rewired bacterial gene networks. |
http://www.ncbi.nlm.nih.gov/pubmed/18421347 |
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 | ||
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