PortEco Microarray Pipeline

Title/Dataset Description	Reference	Platform	GEO Accession	ArrayExpress Accession	Data loaded	Curation completed	Notes	category/subcat	date started
Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions				E-MEXP-3800
				E-MEXP-3799
				E-GEOD-43325
				E-GEOD-29076
				E-GEOD-42702
				E-GEOD-34991
				E-GEOD-37026
				E-MTAB-1347
				E-GEOD-21820
				E-GEOD-22285
				E-GEOD-40693
				E-GEOD-40648
				E-GEOD-21652
				E-GEOD-36779
				E-GEOD-20380
				E-GEOD-39607			JD: skipped it
				E-GEOD-30679
				E-GEOD-30692
				E-GEOD-30424
				E-GEOD-34046
				E-GEOD-21857
				E-TABM-86
				E-GEOD-29803
				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	http://www.ncbi.nlm.nih.gov/pubmed/22331529 http://onlinelibrary.wiley.com/doi/10.1002/bem.21709/full	Affymetrix E. coli Genome 2.0 Array	GSE35371	E-GEOD-35371	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt needs c3-c4	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 http://www.pnas.org/content/109/24/9487.long	Affymetrix E. coli Genome 2.0 Array	GSE30639	E-GEOD-30639	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt needs c3-c4	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.	http://www.ncbi.nlm.nih.gov/pubmed/20886356 http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-2609	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt	biofilm/urine	02/26/13
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 http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt	ETOH shock/rpoS	02/26/13
Expression data from E. coli cells overexpressing GraL for short and long periods of time	http://www.ncbi.nlm.nih.gov/pubmed/20008510 http://nar.oxfordjournals.org/content/38/5/1636.long	Affymetrix E. coli Genome 2.0 Array	GSE15406 (GSE15404, GSE15405)	E-GEOD-15406 (E-GEOD-15404, E-GEOD-15405)	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt needs c1-c4	Overexpression/????	02/26/13
Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate	http://www.ncbi.nlm.nih.gov/pubmed/20501031 http://www.ingentaconnect.com/content/iafp/jfp/2010/00000073/00000005/art00002?token=0052126e147e442f2067217a763b442e237b4524406a687627502b333e3568263c2b40304a62d62140	Affymetrix E. coli Genome 2.0 Array	GSE17519	E-GEOD-17519	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt c1-c4	benzoate/??????	02/26/13
E.coli response to Antimicrobial Arylamides	http://www.ncbi.nlm.nih.gov/pubmed/21844313 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195038/#B7	Affymetrix E. coli Genome 2.0 Array	GSE31140	E-GEOD-31140	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt needs c3-c4	antimicrobial agent/transcription profile	02/26/13
Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock	http://globethesis.com/?t=1100360275976128	Affymetrix E. coli Genome 2.0 Array	GSE17465	E-GEOD-17465	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt needs c1-c4	Salt tolerance/Radiation resistance	02/26/13
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 http://iai.asm.org/content/75/2/966.long	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 http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.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.	http://www.ncbi.nlm.nih.gov/pubmed/20444967 http://jcm.asm.org/content/48/7/2449.full	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 http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt needs c1-c4	urine/biofilm	02/27/13
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