PortEco Microarray Pipeline: Difference between revisions

Latest revision as of 21:36, 31 July 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		E-MEXP-3800	loaded 07/16/13		JD E-MEXP-3800.idf.txt E-MEXP-3800.sdrf.txt needs c1-4	Media comparisons/Culturing history	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		E-MEXP-3799	loaded 07/16/13		JD E-MEXP-3799.idf.txt E-MEXP-3799.sdrf.txt needs c1-4	Media comparisons/H2O2	03/20/13
Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor	no publication	Affymetrix E. coli Genome 2.0 Array	GSE43325	E-GEOD-43325	loaded 07/15/13		JD E-GEOD-43325.idf.txt E-GEOD-43325.sdrf.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	Affymetrix E. coli Genome 2.0 Array	GSE29076	E-GEOD-29076	loaded 07/16/13		JD E-GEOD-29076.idf.txt E-GEOD-29076.sdrf.txt needs c1-4	Nitric oxide/transcription profiling	03/21/13
Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism	PMID:23292772^[1] jbact	Affymetrix E. coli Genome 2.0 Array	GSE42702	E-GEOD-427020	loaded 06/06/13	C1-C4 Complete AMS	JD: no cel files and only norm intensity values E-GEOD-42702.idf.txt E-GEOD-42702.sdrf.txt needs c1-4	Stress response/Parkinson's disease	03/21/13
Fucose sensing regulates bacterial intestinal colonization	PMID:23160491^[2] nature	Affymetrix E. coli Genome 2.0 Array	GSE34991	E-GEOD-34991	loaded 6/27/13		JD E-GEOD-34991.idf.txt E-GEOD-34991.sdrf.txt needs c1-4	Fucose sensing/colonization	03/21/13
Global transcriptional responses to the bacteriocin colicin M in Escherichia coli	PMID:23421615^[3] BMCMicro	Affymetrix E. coli Genome 2.0 Array	GSE37026	E-GEOD-37026	loaded 7/01/13		JD E-GEOD-37026.idf.txt E-GEOD-37026.sdrf.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	PMID:23222720^[4] jbact	Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]		E-MTAB-1347	loaded 07/02/13		JD E-MTAB-1347.idf.txt E-MTAB-1347.sdrf.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)	PMID:23071782^[5] plosone	Affymetrix E. coli Genome 2.0 Array	GSE21820	E-GEOD-21820	loaded 06/06/13	C1-C4 Complete AMS	JD E-GEOD-21820.idf.txt E-GEOD-21820.sdrf.txt needs c1-4	Starvation/Phosphate	03/21/13
Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence	PMID:23163871^[6] FEMS_IMM	Affymetrix E. coli Genome 2.0 Array	GSE22285	E-GEOD-22285	loaded 07/02/13		JD E-GEOD-22285.idf.txt E-GEOD-22285.sdrf.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	PMID:23183978^[7] AEM	Affymetrix E. coli Genome 2.0 Array	GSM999249	E-GEOD-40693	loaded 5/16/13	C1-4 done, AMS 05/15/13 DAS sent idf, sdrf to JD	JD E-GEOD-40693.idf.txt E-GEOD-40693.sdrf.txt needs c1-4	Antimicrobial agent/transcription profiling	03/21/13	+	+ Cinnamaldehyde	+	complete 5/17/13
Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression	PMID:23472115^[8] plosone	Affymetrix E. coli Genome 2.0 Array	GSE40648	E-GEOD-40648	loaded 6/25/13		JD E-GEOD-40648.idf.txt E-GEOD-40648.sdrf.txt	microgravity/transcript profiling	03/22/13
Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli	PMID:22869698^[9] pnas	Affymetrix E. coli Genome 2.0 Array	GSM540098	E-GEOD-21652	loaded 07/10/13		JD E-GEOD-21652.idf.txt E-GEOD-21652.sdrf.txt needs c3-4	Biotechnology/Transcript profiling	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	GSE20380	E-GEOD-20380	loaded 07/15/13		JD E-GEOD-20380.idf.txt E-GEOD-20380.sdrf.txt ready to load?	bile acids/transcript profiling	03/22/13
Expression data from QdNOs treated Escherichia coli	no publication	Affymetrix E. coli Genome 2.0 Array	GSE39607	E-GEOD-39607	loaded 07/15/13		JD E-GEOD-39607.idf.txt E-GEOD-39607.sdrf.txt needs c4	Antimicrobial agent/transcript profiling	03/22/13
Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression	PMID:23106382^[10] fmes-micro	Affymetrix E. coli Genome 2.0 Array	GSM760801	E-GEOD-30679	loaded 5/26/13	05/24/13 - DAS	JD E-GEOD-30679.idf.txt E-GEOD-30679.sdrf.txt needs c3-4	diglutathionylspermidine/transcription profiling	03/22/13	+	+	+	complete 05/30/13
Antitoxin DinJ influences the general stress response through transcript stabilizer CspE	PMID:22026739^[11] env_microb	Affymetrix E. coli Genome 2.0 Array	GSM761209	E-GEOD-30692	loaded 06/07/13	07/10/13 - DAS	JD E-GEOD-30692.idf.txt E-GEOD-30692.sdrf.txt needs c3	Toxin-antitoxin system/Stress response	03/22/13	+	+	+	complete 07/10/13
Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.	PMID:22274708^[12] AMB	Affymetrix E. coli Genome 2.0 Array	GSE30424	E-GEOD-30424	loaded 07/03/13		JD E-GEOD-30424.idf.txt E-GEOD-30424.sdrf.txt ready to load?	biofilm/Indole	03/22/13
Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7	PMID:22589288^[13] Bio	Affymetrix E. coli Genome 2.0 Array	GSE34046	E-GEOD-34046	loaded 6/27/13		JD E-GEOD-34046.idf.txt E-GEOD-34046.sdrf.txt ready to load?	virulence/Ethanolamine	03/22/13
				E-GEOD-21857	loaded (partially, as E-GEOD-21820)		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	PMID:21703240^[14] BBRC	Affymetrix E. coli Genome 2.0 Array	GSE29803	E-GEOD-29803	loaded 07/10/13		JD E-GEOD-29803.idf.txt E-GEOD-29803.sdrf.txt needs c3-4?	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	PMID:22331529^[15]	Affymetrix E. coli Genome 2.0 Array	GSE35371	E-GEOD-35371	loaded 6/28/13		JD E-GEOD-35371.idf.txt 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	PMID:22645336^[16] PNAS	Affymetrix E. coli Genome 2.0 Array	GSE30639	E-GEOD-30639	loaded 6/27/13		JD E-GEOD-30639.idf.txt E-GEOD-30639.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.	PMID:20886356^[17] mgg	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-2609	loaded 03/25/13	03/20/13 - DAS	JD E-MEXP-2609.idf.txt E-MEXP-2609.sdrf.txt	biofilm/urine	02/26/13	+	+	+	complete (redone 5/9/13)
Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase	no publication listed	Affymetrix GeneChip E.coli Genome 2.0 Array	GSE17526	E-GEOD-17526	loaded 5/14/13	3/30/2013 - DAS	JD E-GEOD-17526.idf.txt E-GEOD-17526.sdrf.txt	Ethanol shock/rpoS	02/26/13	+	+	+	complete on 5/15/13
Expression data from E. coli cells overexpressing GraL for short and long periods of time	PMID:20008510^[18]	Affymetrix E. coli Genome 2.0 Array	GSE15406 (GSE15404, GSE15405)	E-GEOD-15406 (E-GEOD-15404, E-GEOD-15405)	loaded 6/28/13		JD E-GEOD-15406.idf.txt E-GEOD-15406.sdrf.txt needs c1-c4	Overexpression/????	02/26/13
Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate	PMID:20501031^[19]	Affymetrix E. coli Genome 2.0 Array	GSE17519	E-GEOD-17519	loaded 07/11/13		JD E-GEOD-17519.idf.txt E-GEOD-17519.sdrf.txt c1-c4	benzoate/transcript profiling	02/26/13
E. coli response to Antimicrobial Arylamides	PMID:21844313^[20]	Affymetrix E. coli Genome 2.0 Array	GSE31140	E-GEOD-31140	loaded 03/19/13 re-loaded 04/14/13	3/17/13 - DAS sdrf file at AE didn't have a column for Sample Name	JD E-GEOD-31140.sdrf.txt E-GEOD-31140.idf.txt needs c3-c4	antimicrobial agent/transcription profile	02/26/13	+	+	+	complete (redone 05/08/13)
Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock	pmid paper	Affymetrix E. coli Genome 2.0 Array	GSE17465	E-GEOD-17465	loaded 07/16/13		JD E-GEOD-17465.sdrf.txt E-GEOD-17465.sidf.txt needs c1-c4	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.	PMID:22008207^[21]	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MTAB-623	loaded 07/09/13		JD E-MTAB-623.idf.txt E-MTAB-623.sdrf.txt needs c3-c4	cold-shock/water activity	02/27/13
Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.	PMID:17145952^[22]	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-926	loaded 6/27/13		JD E-MEXP-926.idf.txt 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.	PMID:20444967^[23]	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-2298	loaded 6/27/13		JD E-MEXP-2298.idf.txt E-MEXP-2298.sdrf.txt needs c1-c4	urine/biofilm	02/27/13
Impact of cranberry on Escherichia coli cellular surface characteristics.	PMID:18957286^[24]	Affymetrix E. coli Genome 2.0 Array	GSE12554	E-GEOD-12554	loaded 07/03/13		JD E-GEOD-12554.idf.txt E-GEOD-12554.sdrf.txt needs c3-c4	antibacterial agent/cranberry juice	02/27/13
Evolvability and hierarchy in rewired bacterial gene networks.	PMID:18421347^[25]	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-732	loaded 6/28/13		JD E-MEXP-732.idf.txt E-MEXP-732.sdrf.txt needs c1-c4	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	23472115 plosone	Affymetrix GeneChip E.coli Genome 2.0 Array	GSE34275	E-GEOD-34275	loaded 6/25/13		JD E-GEOD-34275.idf.txt E-GEOD-34275.sdrf.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	PMID:22018139^[26]	Affymetrix E. coli Genome 2.0 Array	GSE29440	E-GEOD-29440	loaded 06/24/13		JD E-GEOD-29440.idf.txt E-GEOD-29440.sdrf.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	PMID:22018139^[26] www.amb-express.com PMID:22134216^[27] pubs.rsc.org	Affymetrix E. coli Genome 2.0 Array	GSE28412	E-GEOD-28412	loaded 06/07/13		JD E-GEOD-28412.idf.txt E-GEOD-28412.sdrf.txt needs c1-c4	stress/recombinant proteins	02/28/13
Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture	PMID:22018139^[26]	Affymetrix E. coli Genome 2.0 Array	GSE29439	E-GEOD-29439	loaded 06/24/13		JD E-GEOD-29439.idf.txt E-GEOD-29439.sdrf.txt needs c1-c4	recombinant proteins/transcript profiling	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	loaded 07/16/13		JD E-GEOD-29486.idf.txt 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.	PMID:23090957^[28] IAI	Affymetrix E. coli Genome 2.0 Array	GSE28399	E-GEOD-28399	loaded on 5/16/13	4/3/13 - DAS	JD: missing one cel file E-GEOD-28399.idf.txt E-GEOD-28399.sdrf.txt missing one cel file	UPEC/high osmolarity	02/28/13	+	+ OsmolarityUPEC	+	complete 5/17/13
Metabolic and transcriptional response to cofactor perturbations in Escherichia coli	PMID:20299454^[29] PMC2878514	Affymetrix E. coli Genome 2.0 Array	GSE20374	E-GEOD-20374	loaded 06/07/13	C1-C4 Completed AMS	JD GEOD-20374.idf.txt E-GEOD-20374.sdrf.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	PMID:19806199^[30]	Affymetrix E. coli Genome 2.0 Array	GSE14796	E-GEOD-14796	loaded 06/24/13	07/08/2013 - DAS 07/09/2013 - sent to JD	JD E-GEOD-14796.idf.txt E-GEOD-14796.sdrf.txt	Colony/control or L-form	03/01/13	+	+	+	complete 07/10/13
Identification of genes induced on nitrate, role of OxyR	PMID:22539721^[31] Science	Affymetrix E. coli Genome 2.0 Array	GSE24524	E-GEOD-24524	loaded 07/03/13		JD E-GEOD-24524.idf.txt E-GEOD-24524.sdrf.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	PMID:22144490^[32] PMC3264324	Affymetrix E. coli Genome 2.0 Array	GSE33895	E-GEOD-33895	loaded 6/25/13		JD E-GEOD-33895.idf.txt E-GEOD-33895.sdrf.txt needs c2-c4	virulence/His kinase	03/01/13
Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa	PMID:22101045^[33]	Affymetrix E. coli Genome 2.0 Array	GSE26931	E-GEOD-26931	data are loaded in database 03/19/13 re-loaded 04/15/13	used annot from batch loading	JD E-GEOD-26931.idf.txt E-GEOD-26931.sdrf.txt needs c1-c4 only loading 4 slides, the ones that are assayed on coli platform	mixed culture/transcript profiling	03/01/13	+ (with GSE26932)	+ (with GSE26932)	+ (with GSE26932)	complete (redone 5/10/13)
A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.	PMID:21169565^[34] PMC3047162	Affymetrix E. coli Genome 2.0 Array	GSE21551	E-GEOD-21551	loaded 03/19/13 re-loaded 04/13/13	03-11-13 - DAS (waiting to hear about strains but OK to load)	JD GEOD-21551.idf.txt E-GEOD-21551.sdrf.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 of gene expression	03/01/13	+	+	+	complete (redone 5/8/13)
Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol	PMID:22936779^[35] PMID:22936779^[35]	Affymetrix E. coli Genome 2.0 Array	GSE34631	E-GEOD-34631	loaded 03/19/13 re-loaded 04/14/13	03/12/13 - DAS	JD GEOD-34631.idf.txt E-GEOD-34631.sdrf.txt needs c3-4: done	Carbon sources/Enzyme evolution	03/01/13	+	+	+	complete (redone 5/7/13)
Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans	PMID:22792156^[36] PMC3390347	Affymetrix E. coli Genome 2.0 Array	GSE30441	E-GEOD-30441	loaded 5/16/13	c1-4 done, AMS 05/15/13 DAS sent idf, sdrf to JD	JD GEOD-30441.idf.txt GEOD-30441.sdrf.txt	Stress resistance/EtOH	03/01/13	+	+ Ethanol-irrE	+	complete 5/17/13
First insights into the unexplored two-component system YehU/YehT in Escherichia coli.	PMID:22685278^[37] PMC3416263	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MTAB-984	loaded 6/27/13		JD E-MTAB-984.idf.txt E-MTAB-984.sdrf.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	PMID:22684885^[38] biotech_bioeng	Affymetrix E. coli Genome 2.0 Array	GSE35100	E-GEOD-35100	loaded 03/25/13 re-loaded 04/13/13	03/20/13 - DAS	JD E-GEOD-35100.idf.txt E-GEOD-35100.sdrf.txt	Chemical effects/Mutant vs Wild-type	03/01/13	+	+	+	complete (redone 5/7/13)
Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine	PMID:22101045^[33] PMC3255741	Affymetrix E. coli Genome 2.0 Array	GSE)	E-GEOD-26932	data loaded 03/19/13 re-loaded 04/15/13	used annotation from batch loading	JD E-GEOD-26932.idf.txt E-GEOD-26932.sdrf.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)	complete (redone 5/10/13)
Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock	PMID:23247721^[39] pubs.rsc.org	Affymetrix E. coli Genome 2.0 Array	GSE30838	E-GEOD-30838	completed, 03/18/13 re-loaded 04/15/13	03/14/13 - DAS DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.	JD E-GEOD-30838.idf.txt E-GEOD-30838.sdrf.txt needs c1-4: done pUC-A1501 described in PMID:19799945^[40]	glyphosate shock/transcriptional profiling	03/04/13	+	+	+	complete (redone 5/8/13)
Relative expression profiling of ycdC knockout strain secreting HlyA protein	PMID:22505047^[41] full text	Affymetrix E. coli Genome 2.0 Array	GSE29266	E-GEOD-29266	loaded 07/10/13		JD E-GEOD-29266.idf.txt E-GEOD-29266.sdrf.txt needs c1-c4	biotechnology/protein secretion	03/04/13
Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis	PMID:22210763^[42] PMC3294818	Affymetrix E. coli Genome 2.0 Array	GSE23417	E-GEOD-23417	loaded 07/15/13		JD E-GEOD-23417.idf.txt E-GEOD-23417.sdrf.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^[43]	Affymetrix E. coli Genome 2.0 Array	GSE11303	E-GEOD-11303	loaded 03/18/13	03/13/2013 - DAS	JD E-GEOD-11303.idf.txt E-GEOD-11303.sdrf.txt needs c3-4: done	stress/zinc or Chemical effects/zinc	03/04/13	+	+	+	complete (redone 5/9/13)
Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol	PMID:22389366^[44] PMC3346451	Affymetrix E. coli Genome 2.0 Array	GSE35797	E-GEOD-35797	loaded 07/15/13	AMS c1-4 done	JD E-GEOD-35797.idf.txt E-GEOD-35797.sdrf.txt needs c3-4	Biofilms/drug treatment	03/04/13
Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.	PMID:21398637^[45] PMC3141248	Affymetrix E. coli Genome 2.0 Array	GSE22207	E-GEOD-22207	loaded 07/03/13		JD E-GEOD-22207.idf.txt E-GEOD-22207.sdrf.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	PMID:21255366^[46] PMC3158428	Affymetrix E. coli Genome 2.0 Array	GSE21604	E-GEOD-21604	loaded 06/24/13		JD E-GEOD-21604.idf.txt E-GEOD-21604.sdfr.txt needs c2-4	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.	PMID:20855516^[47] PMC2981326	Affymetrix E. coli Genome 2.0 Array	GSE21893	E-GEOD-21893	loaded 07/11/13		JD E-GEOD-21893.idf.txt E-GEOD-21893.sdrf.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	PMID:22221537^[48] full text	Affymetrix E. coli Genome 2.0 Array	GSE34028	E-GEOD-34028	loaded 03/19/13 re-loaded 04/14/13	03/12/2013 - DAS	JD E-GEOD-34028.idf.txt E-GEOD-34028.sdrf.txt needs c3-4: DAS added 3/12/2013	Persister cells/Mutant vs Wild-type	03/05/13	+	+	+	complete (redone 5/7/13)
Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin	PMID:22221537^[48] full text	Affymetrix E. coli Genome 2.0 Array	GSE31054	E-GEOD-31054	loaded 07/09/13		JD E-GEOD-31054.idf.txt E-GEOD-31054.sdrf.txt needs c3-4	Persister cells/Stress resistance	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	PMID:22047137^[49] full text	Affymetrix E. coli Genome 2.0 Array	GSE28193	E-GEOD-28193	loaded 6/28/13		JD E-GEOD-28193.idf.txt E-GEOD-28193.sdrf.txt needs c3-4	biofilm/honey	03/05/13
The E. coli deletion mutant of the nusB gene	PMID:21873492^[50]	Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]		E-MEXP-3335	loaded 5/15/13	4/4/13 - DAS	JD E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt needs c3-4	tRNA modificaton/transcript profiling	03/05/13	+	+	+	complete 5/16/13
E. coli ygjD gene temperature sensitive mutant incubated at 37 oC	PMID:21873492^[50] JB	Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]		E-MEXP-3334	loaded 6/28/13		JD E-MEXP-3334.idf.txt E-MEXP-3334.sdrf.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.	PMID:21873492^[50] JB	Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]		E-MEXP-3333	loaded 6/28/13		JD E-MEXP-3333.idf.txt E-MEXP-3333.sdrf.txt needs c2-4	tRNA modification/transcript profiling	03/05/13
Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages	PMID:21221972^[51] PMC3158427	Affymetrix E. coli Genome 2.0 Array	GSE19953	E-GEOD-19953	loaded 06/06/13	C1-C4 Complete AMS	JD E-GEOD-19953.idf.txt E-GEOD-19953.sdrf.txt needs c3-4	EHEC/biofilm	03/05/13
An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.	PMID:20005205^[52]	Affymetrix E. coli Genome 2.0 Array	GSE18972	E-GEOD-18972	loaded 03/19/13 re-loaded 04/13/13	03/11/13 - DAS	JD E-GEOD-18972.idf.txt E-GEOD-18972.sdrf.txt needs c1-4 no cel files in ae	biofuel/glycerol	03/05/13	+	+	+	complete (redone 5/8/13)
QseA regulation of virulence factors in EHEC	PMID:20444105^[53] PMC2936457	Affymetrix E. coli Genome 2.0 Array	GSE18118	E-GEOD-18118	loaded 07/10/13		JD E-GEOD-18118.idf.txt 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	PMID:19060153^[54] PMC2632003	Affymetrix E. coli Genome 2.0 Array	GSE12701	E-GEOD-12701	was already loaded as part of publication: "Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae." together with E-GEOD-11932	c1-4 done, AMS 05/15/13 DAS sent idf, sdrf to JD	JD E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt needs c2-4 modified matrix file Absent->A, ...	biofilm/toxin-antitoxin system	03/05/13	+	+	+	complete
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	loaded 6/25/13		JD E-GEOD-44273.idf.txt E-GEOD-44273.sdrf.txt needs c1-4	persistence/transcript profiling	03/06/13
Overexpression of BglJ and LeuO in Escherichia coli K12	PMID:22295907^[55] full text	Affymetrix E. coli Genome 2.0 Array	GSE34023		loaded 07/08/13		JD: dataset not in ae, idf/sdrf made from scratch E-GEOD-34023.idf.txt E-GEOD-34023.sdrf.txt needs c1-4	Virulence/Regulation of gene expression	03/06/13
Expression data from laboratory evolution of Escherichia coli on lactate or glycerol	PMID:16204189^[56] PMC1240078	Ecoli_ASv2	GSE33147	E-GEOD-33147	loaded 05/14/13	C1-4 done, AMS sent idf, sdrf to JD on 5/13/13	JD E-GEOD-33147.idf.txt E-GEOD-33147.sdrf.txt needs c3-4	evolution/carbon source	03/07/13	+	+	+	complete
Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.	PMID:17112383^[57] PMC1664580	Ecoli_ASv2	GSE5239	E-GEOD-5239	loaded 05/27/13	loaded 05/26/13	JD dataset has no cel files and only intensity values! E-GEOD-5239.idf.txt E-GEOD-5239.sdrf.txt	plasmid/metabolism	03/07/13	+	+	- (no cel files)	complete (5/31/13)
Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains	PMID:17768236^[58] full text	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)	loaded 06/07/13	C1-4 done, AMS	JD E-GEOD-7398.idf.txt E-GEOD-7398.sdrf.txt needs c1-4	growth phase/fis	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	in process		JD: can't figure out how the experiment was done. E-TABM-103.idf.txt E-TABM-103.sdrf.txt		03/07/13
Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli	PMID:15705577^[59] JB	Ecoli_ASv2	GSE2037	E-GEOD-2037	loaded 6/28/13		JD E-GEOD-2037.idf.txt E-GEOD-2037.sdrf.txt needs c3-4 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.	PMID:17576668^[60] PMC1935009	Ecoli_ASv2	GSE5818	E-GEOD-5818	loaded on 5/17/13	03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)	JD: no cel files available E-GEOD-5818.idf.txt 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) 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	+	+	no - no cel files available	complete 5/17/13
Enterobactin is required for biofilm development in reduced-genome Escherichia coli	PMID:21980953^[61] full text	Ecoli_ASv2		E-MEXP-1408	loaded 05/30/13	05/22/13 - DAS	JD E-MEXP-1408.idf.txt E-MEXP-1408.sdrf.txt needs c1-4	biofilm/transcription profiling DAS suggests biofilm/Reduced genome	03/08/13	+	+	+	complete 05/30/13
Indole cell signaling occurs primarily at low temperatures in Escherichia coli	PMID:18528414^[62]	Ecoli_ASv2 and E_coli_2	GSE9923	E-GEOD-9923	loaded 07/03/13		JD E-GEOD-9923.idf.txt 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	PMID:16199566^[63] PMC1251601	Ecoli_ASv2	GSE3105	E-GEOD-3105	loaded 5/16/13	04/16/13 - DAS DAS sent idf, sdrf to JD 05/14/13	JD: no cel files available E-GEOD-3105.idf.txt E-GEOD-3105.sdrf.txt	iron/non-coding RNA	03/08/13	+	+	no: no cel files	complete 5/17/13
sigma32 over-expression in E. coli	PMID:15757896^[64] JBC	Ecoli_ASv2	GSE2140	E-GEOD-2140	loaded 05/31/13	05/26/13 - DAS	JD E-GEOD-2140.idf.txt E-GEOD-2140.sdrf.txt needs c2-4 no cel files available	sigma factor/transcription profiling	03/08/13	+	+	- (no cel files)	complete (5/31/13)
Temporal gene-expression in Escherichia coli K-12 biofilms	PMID:17222132^[65] full text	Ecoli_ASv2	GSE3905	E-GEOD-3905	loaded 07/11/13		JD no cel file available E-GEOD-3905.idf.txt E-GEOD-3905.sdrf.txt needs c3-4	biofilm/transcription profiling	03/08/13
Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation	PMID:20809290^[66] Full Text	Ecoli_ASv2		E-MEXP-1001	loaded 05/30/13	05/27/13 - DAS	JD E-MEXP-1001.idf.txt E-MEXP-1001.sdrf.txt needs c3-4	biofilm/F- phenocopy	03/11/13	+	+	+	complete (06/05/13)
Indole is an inter-species biofilm signal mediated by SdiA	PMID:17511876^[67] PMC1899176	Ecoli_ASv2	GSE4562	E-GEOD-4562	loaded 07/03/13		JD E-GEOD-4562.idf.txt E-GEOD-4562.sdrf.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	PMID:17557827^[68] PMC1952038	Ecoli_ASv2	GSE9203	E-GEOD-9203	loaded 06/97/13	Created C1-C4 AMS	JD: no cel files available E-GEOD-9203.idf.txt E-GEOD-9203.sdrf.txt needs c3-4	Quorum sensing/biofilm	03/11/13
YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling	PMID:16597943^[69] PMC1448992	Ecoli_ASv2	GSE3937	E-GEOD-3937	loaded 5/26/13	05/21/13 - DAS	JD: no cel files available E-GEOD-3937.idf.txt E-GEOD-3937.sdrf.txt needs c3-4	Quorum sensing/biofilm	03/11/13	+	+	- (no cel files)	complete (05/30/13)
Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)	PMID:18309357^[70] The ISME Journal	Ecoli_ASv2	GSE8706	E-GEOD-8706	loaded	C1-4 done, AMS 05/14/13: DAS sent idf/sdrf files to JD	JD E-GEOD-8706.idf.txt E-GEOD-8706.sdrf.txt needs c3-4	Quorum sensing/biofilm	03/11/13	+	+	+	complete (6/05/13)
luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling	PMID:16321939^[71]	Ecoli_ASv2	GSE9587	E-GEOD-9587	loaded 06/06/13)	C1-C4 Complete AMS	JD: one cel file is corrupted - GSM242209 - had to use chp files given E-GEOD-9587.idf.txt 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. The other dataset is E-GEOD-9582 and it was loaded in 2010.	Quorum sensing/(Mutant/wild-type)	03/12/13
Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli	PMID:18790864^[72] JB	Ecoli_ASv2		E-MEXP-1145	loaded 5/15/13	04/03/13 - DAS	JD: E-MEXP-953 is part of same pub - already in porteco E-MEXP-1145.idf.txt E-MEXP-1145.sdrf.txt	Biofilm/F plasmid	03/12/13	+	+	+	complete 5/15/13
YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport	PMID:16385049^[73]	Ecoli_ASv2	GSE3514	E-GEOD-3514	loaded 07/15/13	AMS c1-4 done	JD: no cel files available E-GEOD-3514.idf.txt E-GEOD-3514.sdrf.txt needs c3-4	Quorum sensing/biofilm	03/12/13
YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity	PMID:17293424^[74] PMC1855844	Ecoli_ASv2	GSE5904	E-GEOD-5904	loaded 07/15/13	AMS c1-4 done	JD: no cel files available E-GEOD-5904.idf.txt E-GEOD-5904.sdrf.txt needs c3-4	Biofilm/transcription profiling	03/12/13
Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803	PMID:17521447^[75]	Ecoli_ASv2	GSE5905	E-GEOD-5905	loaded 07/08/13		JD: no cel files available E-GEOD-5905.idf.txt E-GEOD-5905.sdrf.txt needs c3-4	biofuel/biotechnology	03/12/13
A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS	PMID:22941047^[76] nchembio	Affymetrix E. coli Genome 2.0 Array	GSE36779	E-GEOD-36779	loaded 03/26/13 re-loaded 04/12/13	4/4/13 - DAS	JD E-GEOD-36779.idf.txt E-GEOD-36779.sdrf.txt ready to load? - yes (4/4/13 DAS)	Toxin-antitoxin system/transcription profiling	03/22/13	+	+	+	complete (redone - 5/7/13)
Evolutionary genome engineering using a restriction–modification system	PMID:21785135^[77] PMC3203608	Ecoli_ASv2	GSE21869		the experimental data are loaded: PortEco Publication	C1-4 done, AMS	faked idf/sdrf	Evolution/Parental strain Evolution/Evolved strain Evolution/Mutant	Nov 2012	+	+	+	complete (redone 5/10/13)
Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli	PMID:19909729^[78] bbrc	Affymetrix E. coli Genome 2.0 Array	GSE18852	E-GEOD-18852	reload	yes	JD E-GEOD-18852.idf E-GEOD-18852.sdrf	persister cells/toxin-antitoxin systems	04/01/13	+	+	+	complete (5/14/13)
The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli	PMID:21292161^[79] mol_cell	Affymetrix E. coli Genome 2.0 Array	GSE24875	E-GEOD-24875	reload	yes	JD E-GEOD-24875.idf E-GEOD-24875.sdrf	catabolite repression/non-coding RNA	04/01/13				wasn't missing - did not need to reload
A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP	PMID:16377617^[80] jbc PMID:17921306^[81] jbact	A-GEOD-1246.adf.txt A-GEOD-3051.adf.txt	GSE3591	E-GEOD-3591	reload	yes	JD E-GEOD-3591.idf E-GEOD-3591.sdrf 2-channel	aerobic anaerobic transition/(nitrite/nitrate)	04/01/13	+	+	+	complete (redone 5/9/13)
The PurR regulon in Escherichia coli K-12 MG1655	PMID:21572102^[82] nar	Affymetrix E. coli Genome 2.0 Array	GSE26588	E-GEOD-26588	reload	yes	JD E-GEOD-26588.idf E-GEOD-26588.sdrf	purine metabolism/transcript profiling OR Chemical effects/wild-type vs mutant	04/01/13	+	+	+	complete (redone 5/8/13)
Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal	PMID:21059164^[83] env_micro	Affymetrix E. coli Genome 2.0 Array	GSE22057	E-GEOD-22057	reload	yes	JD E-GEOD-22057.idf E-GEOD-22057.sdrf	biofilm dispersal/transcript profiling	04/01/13	+	+	+	complete (redone 5/8/13)
Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]	PMID:21984790^[84] jbact	Affymetrix E. coli Genome 2.0 Array	GSE30893	E-GEOD-30893	reload	yes	JD E-GEOD-30893.idf E-GEOD-30893.sdrf	type III secretion system/transcript profiling	04/01/13	+	+	+	complete (redone 05/08/13)
Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]	PMID:21930760^[85] infect_immun	Affymetrix E. coli Genome 2.0 Array	GSE28144	E-GEOD-28144	reload	yes	JD E-GEOD-28144.idf E-GEOD-28144.sdrf	biofilms/antioxidants	04/01/13	+	+	+	complete (redone 5/7/13)
Dynamic omics approach identifies nutrition-mediated microbial interactions.	PMID:21058740^[86] j_prot_res	Affymetrix E. coli Genome 2.0 Array	GSE18474	E-GEOD-18474	reload	yes	JD E-GEOD-18474.idf E-GEOD-18474.sdrf load only coli data	co-culture/transcript profiling	04/01/13	+	+	+	complete (redone 5/8/13)
Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD	PMID:20105222^[87] env_micro	Affymetrix E. coli Genome 2.0 Array Affymetrix E. coli Antisense Genome Array	GSE14203	E-GEOD-14203	reload - expression data only	yes	JD E-GEOD-14203.idf E-GEOD-14203.sdrf two platforms - sdrf only contains data for genome 2.0 array	toxin antitoxin systems/transcript profiling	04/01/13	+	+	+	complete (redone 5/9/13)
Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli	PMID:21695201^[88] plosone	Affymetrix GeneChip E.coli Antisense Genome Array		E-MEXP-3191	reload	yes	JD E-MEXP-3191.idf E-MEXP-3191.sdrf	Heat shock/critical high temperature	04/01/13	+	+	+	complete (redone 5/8/13)
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.	PMID:19240136^[89] pmc	A-MEXP-1444		E-MEXP-1872	reload	yes		blue-light response/two-component system		+	+	+	complete (reloaded 5/14/13)
Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine	PMID:22753377^[90] iai	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-584	reload	yes	JD E-MEXP-584.idf E-MEXP-584.sdrf	Asymptomatic Bacteriuria/transcription profiling	04/01/13	+	=	+	complete (redone 5/9/13)
Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC	PMID:19240136^[89] pmc	A-MEXP-1444		E-MEXP-1877	reload	yes		blue-light response/two-component system		+	+	+	complete (reloaded 5/14/13)
Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110	PMID:18302792	Affymetrix E. coli Antisense Genome Array	GSE4778	E-GEOD-4778	reloaded 6/25/13		redoing this data set because there was a problem with the original loading	Stress/pH (external)	06/21/2013	+	+	+	complete 06/25/13
changes of global gene expression in E. coli during an oxygen shift	pmid:15129285 nature	Affymetrix E. coli Antisense Genome Array	GSE1121 GSE1106 GSE1107	E-GEOD-1121	reloaded 6/28/13	yes	reloaded due to error during original loading	(aerobic/anaerobic)/(mutant/wild-type)		+	+	+	6/28/13
Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation	PMID:17504765	Affymetrix E. coli Antisense Genome Array	GSE6425	E-GEOD-6425	reloaded 7/02/13	yes	redoing this data set because there was a problem with the original loading	Strain comparison/(Anaerobic growth/Aerobic Growth)		+	+	+	complete 07/02/13
Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series	PMID:17504765	Affymetrix E. coli Antisense Genome Array	GSE6426	E-GEOD-6426	reloaded 7/02/13	yes	redoing this data set because there was a problem with the original loading	Strain comparison/cecum		+	+	+	complete 07/02/13
			GSE26591	E-GEOD-26591	loaded (partially, as E-GEOD-26588)		JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded
Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach	PMID:23536188^[91] jbc	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-3639	loaded 07/16/13		JD: E-MEXP-3639.idf.txt E-MEXP-3639.sdrf.txt needs c1 - c4	bleach/transcription profiling	07/16/13
Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants	pmid paper	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-3811	loaded 07/16/13		JD needs c1-4	nucleoid/transcript profiling	07/16/13
Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli	pmid paper	Affymetrix GeneChip E.coli Antisense Genome Array Affymetrix GeneChip E.coli Genome 2.0 Array	GSE9923	E-GEOD-9923	loaded (partially)		JD: 4 slides from antisense platform are not loaded
Enterohemorrhagic Escherichia coli (EHEC) 86-24 double deletions of kdpE and cra grown in DMEM	PMID:23524613^[92]	Affymetrix GeneChip E.coli Genome 2.0 Array	GSE43659	E-GEOD-43659	loaded 07/16/13	07/23/13 - DAS updated idf,sdrf	JD: needs c1-c4	virulence/transcript profiling	07/16/13	+	+	+	07/23/13
Expression data from Avian Pathogenic Escherichia coli	not published	Affymetrix GeneChip E.coli Genome 2.0 Array	GSE48015	E-GEOD-48015	loaded 07/17/13			APEC/transcript profiling	07/17/13
Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482	not published	Affymetrix GeneChip E.coli Genome 2.0 Array	GSE47418	E-GEOD-47418	loaded 07/17/13			EHEC/co-culture	07/17/13
Expression profiling of wt and ydcR mutant strains	not published	E. coli Genome 2.0 Array	GSE48776	not yet in AE	in process		JD: wait for mage_tab files This is part of a superset: GSE48832, which also includes hts dataset GSE48829.
edit table

↑ Messaoudi, N et al. (2013) Global stress response in a prokaryotic model of DJ-1-associated Parkinsonism. J. Bacteriol. 195 1167-78 PubMed
↑ Pacheco, AR et al. (2012) Fucose sensing regulates bacterial intestinal colonization. Nature 492 113-7 PubMed
↑ Kamenšek, S & Žgur-Bertok, D (2013) Global transcriptional responses to the bacteriocin colicin M in Escherichia coli. BMC Microbiol. 13 42 PubMed
↑ Fried, L et al. (2013) Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli. J. Bacteriol. 195 807-15 PubMed
↑ Yang, C et al. (2012) Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli. PLoS ONE 7 e47314 PubMed
↑ Bansal, T et al. (2012) Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence. FEMS Immunol. Med. Microbiol. 66 399-410 PubMed
↑ Visvalingam, J et al. (2013) Examination of the genome-wide transcriptional response of Escherichia coli O157:H7 to cinnamaldehyde exposure. Appl. Environ. Microbiol. 79 942-50 PubMed
↑ Arunasri, K et al. (2013) Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression. PLoS ONE 8 e57860 PubMed
↑ Santos, CN et al. (2012) Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 109 13538-43 PubMed
↑ Chattopadhyay, MK et al. (2013) Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression. FEMS Microbiol. Lett. 338 132-40 PubMed
↑ Hu, Y et al. (2012) Antitoxin DinJ influences the general stress response through transcript stabilizer CspE. Environ. Microbiol. 14 669-79 PubMed
↑ Lee, JH et al. (2012) Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation. Appl. Microbiol. Biotechnol. 96 1071-8 PubMed
↑ Kendall, MM et al. (2012) Ethanolamine controls expression of genes encoding components involved in interkingdom signaling and virulence in enterohemorrhagic Escherichia coli O157:H7. MBio 3 PubMed
↑ Ma, Q & Wood, TK (2011) Protein acetylation in prokaryotes increases stress resistance. Biochem. Biophys. Res. Commun. 410 846-51 PubMed
↑ 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
↑ Le Gac, M et al. (2012) Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 109 9487-92 PubMed
↑ Hancock, V et al. (2010) Functional genomics of probiotic Escherichia coli Nissle 1917 and 83972, and UPEC strain CFT073: comparison of transcriptomes, growth and biofilm formation. Mol. Genet. Genomics 284 437-54 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
↑ ^26.0 ^26.1 ^26.2 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
↑ Withman, B et al. (2013) Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea. Infect. Immun. 81 80-9 PubMed
↑ Holm, AK et al. (2010) Metabolic and transcriptional response to cofactor perturbations in Escherichia coli. J. Biol. Chem. 285 17498-506 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
↑ Seth, D et al. (2012) Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR. Science 336 470-3 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
↑ ^33.0 ^33.1 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
↑ Strader, MB et al. (2011) A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. Mol. Cell Proteomics 10 M110.005199 PubMed
↑ ^35.0 ^35.1 Nam, H et al. (2012) Network context and selection in the evolution to enzyme specificity. Science 337 1101-4 PubMed
↑ Chen, T et al. (2012) Significant rewiring of the transcriptome and proteome of an Escherichia coli strain harboring a tailored exogenous global regulator IrrE. PLoS ONE 7 e37126 PubMed
↑ Kraxenberger, T et al. (2012) First insights into the unexplored two-component system YehU/YehT in Escherichia coli. J. Bacteriol. 194 4272-84 PubMed
↑ Wang, J et al. (2012) Global regulator engineering significantly improved Escherichia coli tolerances toward inhibitors of lignocellulosic hydrolysates. Biotechnol. Bioeng. 109 3133-42 PubMed
↑ Lu, W et al. (2013) Genome-wide transcriptional responses of Escherichia coli to glyphosate, a potent inhibitor of the shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase. Mol Biosyst 9 522-30 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
↑ Gupta, P et al. () A single nucleotide polymorphism in ycdC alters tRNA synthetase expression and results in hypersecretion in Escherichia coli. Biotechnol. Prog. 28 646-53 PubMed
↑ Warner, DM & Levy, SB (2012) SoxS increases the expression of the zinc uptake system ZnuACB in an Escherichia coli murine pyelonephritis model. J. Bacteriol. 194 1177-85 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
↑ Lim, JY et al. (2012) Dimethyl sulfoxide and ethanol elicit increased amyloid biogenesis and amyloid-integrated biofilm formation in Escherichia coli. Appl. Environ. Microbiol. 78 3369-78 PubMed
↑ Maciag, A et al. (2011) In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements. Nucleic Acids Res. 39 5338-55 PubMed
↑ Hong, SH et al. (2010) Engineering global regulator Hha of Escherichia coli to control biofilm dispersal. Microb Biotechnol 3 717-28 PubMed
↑ de Pace, F et al. (2010) The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain. Infect. Immun. 78 4990-8 PubMed
↑ ^48.0 ^48.1 Hong, SH et al. (2012) Bacterial persistence increases as environmental fitness decreases. Microb Biotechnol 5 509-22 PubMed
↑ Lee, JH et al. (2011) Low concentrations of honey reduce biofilm formation, quorum sensing, and virulence in Escherichia coli O157:H7. Biofouling 27 1095-104 PubMed
↑ ^50.0 ^50.1 ^50.2 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
↑ Lee, JH et al. (2011) Transcriptomic analysis for genetic mechanisms of the factors related to biofilm formation in Escherichia coli O157:H7. Curr. Microbiol. 62 1321-30 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
↑ Kendall, MM et al. (2010) The LysR-type regulator QseA regulates both characterized and putative virulence genes in enterohaemorrhagic Escherichia coli O157:H7. Mol. Microbiol. 76 1306-21 PubMed
↑ Kim, Y et al. (2009) Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae. J. Bacteriol. 191 1258-67 PubMed
↑ Stratmann, T et al. (2012) RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants. Mol. Microbiol. 83 1109-23 PubMed
↑ Fong, SS et al. (2005) Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res. 15 1365-72 PubMed
↑ Wang, Z et al. (2006) Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb. Cell Fact. 5 34 PubMed
↑ Bradley, MD et al. (2007) Effects of Fis on Escherichia coli gene expression during different growth stages. Microbiology (Reading, Engl.) 153 2922-40 PubMed
↑ Liu, M et al. (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J. Biol. Chem. 280 15921-7 PubMed
↑ Zhao, K et al. (2007) Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli. Nucleic Acids Res. 35 4441-52 PubMed
↑ May, T & Okabe, S (2011) Enterobactin is required for biofilm development in reduced-genome Escherichia coli. Environ. Microbiol. 13 3149-62 PubMed
↑ Lee, J et al. (2008) Indole cell signaling occurs primarily at low temperatures in Escherichia coli. ISME J 2 1007-23 PubMed
↑ Massé, E et al. (2005) Effect of RyhB small RNA on global iron use in Escherichia coli. J. Bacteriol. 187 6962-71 PubMed
↑ Zhao, K et al. (2005) The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo. J. Biol. Chem. 280 17758-68 PubMed
↑ Domka, J et al. (2007) Temporal gene-expression in Escherichia coli K-12 biofilms. Environ. Microbiol. 9 332-46 PubMed
↑ May, T et al. (2010) Characterization and global gene expression of F- phenocopies during Escherichia coli biofilm formation. Mol. Genet. Genomics 284 333-42 PubMed
↑ Lee, J et al. (2007) Indole is an inter-species biofilm signal mediated by SdiA. BMC Microbiol. 7 42 PubMed
↑ Li, J et al. (2007) Quorum sensing in Escherichia coli is signaled by AI-2/LsrR: effects on small RNA and biofilm architecture. J. Bacteriol. 189 6011-20 PubMed
↑ Domka, J et al. (2006) YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling. Appl. Environ. Microbiol. 72 2449-59 PubMed
↑ Zhang, XS et al. (2008) Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA). ISME J 2 615-31 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
↑ May, T & Okabe, S (2008) Escherichia coli harboring a natural IncF conjugative F plasmid develops complex mature biofilms by stimulating synthesis of colanic acid and Curli. J. Bacteriol. 190 7479-90 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
↑ Zhang, XS et al. (2007) YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity. J. Bacteriol. 189 3051-62 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
↑ Wang, X et al. (2012) A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat. Chem. Biol. 8 855-61 PubMed
↑ Asakura, Y et al. (2011) Evolutionary genome engineering using a restriction-modification system. Nucleic Acids Res. 39 9034-46 PubMed
↑ Kim, Y & Wood, TK (2010) Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem. Biophys. Res. Commun. 391 209-13 PubMed
↑ Beisel, CL & Storz, G (2011) The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol. Cell 41 286-97 PubMed
↑ Constantinidou, C et al. (2006) A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J. Biol. Chem. 281 4802-15 PubMed
↑ Hobman, JL et al. (2007) Comparative genomic hybridization detects secondary chromosomal deletions in Escherichia coli K-12 MG1655 mutants and highlights instability in the flhDC region. J. Bacteriol. 189 8786-92 PubMed
↑ Cho, BK et al. (2011) The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res. 39 6456-64 PubMed
↑ Ma, Q et al. (2011) Engineering a novel c-di-GMP-binding protein for biofilm dispersal. Environ. Microbiol. 13 631-42 PubMed
↑ Kendall, MM et al. (2011) Hfq virulence regulation in enterohemorrhagic Escherichia coli O157:H7 strain 86-24. J. Bacteriol. 193 6843-51 PubMed
↑ Lee, JH et al. (2011) Apple flavonoid phloretin inhibits Escherichia coli O157:H7 biofilm formation and ameliorates colon inflammation in rats. Infect. Immun. 79 4819-27 PubMed
↑ Nakanishi, Y et al. (2011) Dynamic omics approach identifies nutrition-mediated microbial interactions. J. Proteome Res. 10 824-36 PubMed
↑ Kim, Y et al. (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ. Microbiol. 12 1105-21 PubMed
↑ Murata, M et al. (2011) Molecular strategy for survival at a critical high temperature in Eschierichia coli. PLoS ONE 6 e20063 PubMed
↑ ^89.0 ^89.1 Tschowri, N et al. (2009) The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev. 23 522-34 PubMed
↑ Vejborg, RM et al. (2012) Identification of genes important for growth of asymptomatic bacteriuria Escherichia coli in urine. Infect. Immun. 80 3179-88 PubMed
↑ Gray, MJ et al. (2013) NemR is a bleach-sensing transcription factor. J. Biol. Chem. 288 13789-98 PubMed
↑ Njoroge, JW et al. (2013) The interacting Cra and KdpE regulators are involved in the expression of multiple virulence factors in enterohemorrhagic Escherichia coli. J. Bacteriol. 195 2499-508 PubMed

See Help:References for how to manage references in EcoliWiki.

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[PMID:22941047-76] Wang, X et al. (2012) A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat. Chem. Biol. 8 855-61 PubMed

[PMID:21785135-77] Asakura, Y et al. (2011) Evolutionary genome engineering using a restriction-modification system. Nucleic Acids Res. 39 9034-46 PubMed

[PMID:19909729-78] Kim, Y & Wood, TK (2010) Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem. Biophys. Res. Commun. 391 209-13 PubMed

[PMID:21292161-79] Beisel, CL & Storz, G (2011) The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol. Cell 41 286-97 PubMed

[PMID:16377617-80] Constantinidou, C et al. (2006) A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J. Biol. Chem. 281 4802-15 PubMed

[PMID:17921306-81] Hobman, JL et al. (2007) Comparative genomic hybridization detects secondary chromosomal deletions in Escherichia coli K-12 MG1655 mutants and highlights instability in the flhDC region. J. Bacteriol. 189 8786-92 PubMed

[PMID:21572102-82] Cho, BK et al. (2011) The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res. 39 6456-64 PubMed

[PMID:21059164-83] Ma, Q et al. (2011) Engineering a novel c-di-GMP-binding protein for biofilm dispersal. Environ. Microbiol. 13 631-42 PubMed

[PMID:21984790-84] Kendall, MM et al. (2011) Hfq virulence regulation in enterohemorrhagic Escherichia coli O157:H7 strain 86-24. J. Bacteriol. 193 6843-51 PubMed

[PMID:21930760-85] Lee, JH et al. (2011) Apple flavonoid phloretin inhibits Escherichia coli O157:H7 biofilm formation and ameliorates colon inflammation in rats. Infect. Immun. 79 4819-27 PubMed

[PMID:21058740-86] Nakanishi, Y et al. (2011) Dynamic omics approach identifies nutrition-mediated microbial interactions. J. Proteome Res. 10 824-36 PubMed

[PMID:20105222-87] Kim, Y et al. (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ. Microbiol. 12 1105-21 PubMed

[PMID:21695201-88] Murata, M et al. (2011) Molecular strategy for survival at a critical high temperature in Eschierichia coli. PLoS ONE 6 e20063 PubMed

[PMID:19240136-89] 89.0 ^89.1 Tschowri, N et al. (2009) The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev. 23 522-34 PubMed

[PMID:22753377-90] Vejborg, RM et al. (2012) Identification of genes important for growth of asymptomatic bacteriuria Escherichia coli in urine. Infect. Immun. 80 3179-88 PubMed

[PMID:23536188-91] Gray, MJ et al. (2013) NemR is a bleach-sensing transcription factor. J. Biol. Chem. 288 13789-98 PubMed

[PMID:23524613-92] Njoroge, JW et al. (2013) The interacting Cra and KdpE regulators are involved in the expression of multiple virulence factors in enterohemorrhagic Escherichia coli. J. Bacteriol. 195 2499-508 PubMed

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[2]

[3]

[4]

[5]

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[8]

[9]

[10]

[11]

[12]

[13]

[14]

[15]

[16]

[17]

[18]

[19]

[20]

[21]

[22]

[23]

[24]

[25]

[26]

[27]

[28]

[29]

[30]

[31]

[32]

[33]

[34]

[35]

[36]

[37]

[38]

[39]

[40]

[41]

[42]

[43]

[44]

[45]

[46]

[47]

[48]

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[50]

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[52]

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@@ Line 8: / Line 8: @@
 {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K511aabd5a75b9"  class=" tableEdit "
 |-
-!|Title/Dataset Description!!Reference!!Platform!!GEO Accession!!ArrayExpress Accession!!Data loaded!!Curation completed!!Notes!!category/subcat!!date started
+!|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
 |
 |
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3800/ E-MEXP-3800]
 |
-E-MEXP-3800
+loaded 07/16/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3800.idf.txt E-MEXP-3800.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3800.sdrf.txt E-MEXP-3800.sdrf.txt]
-|
+needs c1-4
- JD: skipped it
-|
 |
+Media comparisons/Culturing history
-|-
 |
+/20/13
 |
@@ Line 40: / Line 43: @@
 |
-E-MEXP-3799
+|-
 |
+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
 |
- JD: skipped it
+Affymetrix GeneChip E.coli Genome 2.0 Array
 |
 |
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3799/ E-MEXP-3799]
-|-
 |
+loaded 07/16/13
 |
 |
+JD
-|
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3799.idf.txt E-MEXP-3799.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3799.sdrf.txt E-MEXP-3799.sdrf.txt]
+needs c1-4
 |
-E-GEOD-43325
+Media comparisons/H2O2
 |
+/20/13
 |
@@ Line 74: / Line 80: @@
 |-
 |
+Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor
+|
+no publication
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43325 GSE43325]
 |
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-43325/ E-GEOD-43325]
 |
-E-GEOD-29076
+loaded 07/15/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-43325.idf.txt E-GEOD-43325.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-43325.sdrf.txt E-GEOD-43325.sdrf.txt]
+needs c1-c4; new organism? O55:H7
 |
- JD: skipped it
+Quorum sensing/virulence
+|
+/21/13
+|
+|
 |
@@ Line 95: / Line 114: @@
 |-
 |
+Nitric oxide effect in Escherichia coli O157:H7 EDL933
 |
+no publication
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL3154 Affymetrix E. coli Genome 2.0 Array]
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29076 GSE29076]
 |
-E-GEOD-42702
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29076/ E-GEOD-29076]
 |
+loaded 07/16/13
 |
 |
+JD
-|
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.idf.txt E-GEOD-29076.idf.txt]<br/>[http://expression.porteco.org/MicroArray/data/E-GEOD-29076.sdrf.txt E-GEOD-29076.sdrf.txt]
+needs c1-4
 |
+Nitric oxide/transcription profiling
-|-
 |
+/21/13
 |
@@ Line 124: / Line 144: @@
 |
-E-GEOD-34991
+|-
 |
+Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism
 |
+PMID:23292772 <br/>
+[http://jb.asm.org/content/195/6/1167.long jbact]
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42702 GSE42702]
 |
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-42702/ E-GEOD-427020]
-|-
 |
+loaded 06/06/13
 |
+C1-C4 Complete AMS
 |
+JD: '''no cel files and only norm intensity values'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-42702.idf.txt E-GEOD-42702.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-42702.sdrf.txt E-GEOD-42702.sdrf.txt]
-|
+needs c1-4
 |
-E-GEOD-37026
+Stress response/Parkinson's disease
 |
+/21/13
 |
@@ Line 158: / Line 182: @@
 |-
 |
+Fucose sensing regulates bacterial intestinal colonization
 |
+PMID:23160491
+[http://www.nature.com/nature/journal/v492/n7427/full/nature11623.html#supplementary-information nature]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34991 GSE34991]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34991/ E-GEOD-34991]
+|
+loaded 6/27/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34991.idf.txt E-GEOD-34991.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34991.sdrf.txt E-GEOD-34991.sdrf.txt]
+needs c1-4
 |
-E-MTAB-1347
+Fucose sensing/colonization
 |
+/21/13
 |
@@ Line 179: / Line 217: @@
 |-
 |
+Global transcriptional responses to the bacteriocin colicin M in Escherichia coli
+|
+PMID:23421615
+[http://www.biomedcentral.com/1471-2180/13/42 BMCMicro]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37026 GSE37026]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-37026/ E-GEOD-37026]
 |
+loaded 7/01/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-37026.idf.txt E-GEOD-37026.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-37026.sdrf.txt E-GEOD-37026.sdrf.txt]
+needs c1-4
 |
-E-GEOD-21820
+colicins/transcription profiling
 |
+/21/13
 |
@@ Line 199: / Line 251: @@
 |-
+|
+Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli
+|
+PMID:23222720<br/>
+[http://jb.asm.org/content/195/4/807.full jbact]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
 |
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1347/ E-MTAB-1347]
+|
+loaded 07/02/13
 |
 |
+JD
-|
+[http://expression.porteco.org/MicroArray/data/E-MTAB-1347.idf.txt E-MTAB-1347.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MTAB-1347.sdrf.txt E-MTAB-1347.sdrf.txt]
+ready to load?
 |
-E-GEOD-22285
+Two-component systems/transcript profiling
 |
+/24/13
 |
@@ Line 221: / Line 288: @@
 |-
 |
+Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data)
 |
+PMID:23071782<br/>
+[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047314 plosone]
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21820 GSE21820]
 |
-E-GEOD-40693
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21820/ E-GEOD-21820]
 |
+loaded 06/06/13
 |
+C1-C4 Complete AMS
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21820.idf.txt E-GEOD-21820.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21820.sdrf.txt E-GEOD-21820.sdrf.txt]
+needs c1-4
 |
+Starvation/Phosphate
 |
+/21/13
-|-
 |
@@ Line 248: / Line 321: @@
 |
+|-
 |
-E-GEOD-40648
+Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence
 |
+PMID:23163871<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/1574-695X.12004/full FEMS_IMM]
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22285 GSE22285]
 |
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22285/ E-GEOD-22285]
 |
+loaded 07/02/13
-|-
-|
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-22285.idf.txt E-GEOD-22285.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-22285.sdrf.txt E-GEOD-22285.sdrf.txt]
+needs c1-4
 |
+Virulence/Host factors
 |
-E-GEOD-21652
+/21/13
 |
 |
-|
- JD: skipped it
 |
@@ Line 284: / Line 359: @@
 |-
 |
+Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure
 |
+PMID:23183978<br/>
+[http://aem.asm.org/content/79/3/942.long AEM]
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM999249 GSM999249]
 |
-E-GEOD-36779
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40693/ E-GEOD-40693]
 |
+loaded 5/16/13
 |
+C1-4 done, AMS
+/15/13 DAS sent idf, sdrf to JD
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-40693.idf.txt E-GEOD-40693.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-40693.sdrf.txt E-GEOD-40693.sdrf.txt]
+needs c1-4
 |
+Antimicrobial agent/transcription profiling
 |
+/21/13
-|-
 |
++
 |
++ Cinnamaldehyde
 |
++
 |
+complete 5/17/13
+|-
 |
-E-GEOD-20380
+Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression
 |
+PMID:23472115<br/>
+[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057860 plosone]
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40648 GSE40648]
 |
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-40648/ E-GEOD-40648]
 |
+loaded 6/25/13
-|-
-|
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-40648.idf.txt E-GEOD-40648.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-40648.sdrf.txt E-GEOD-40648.sdrf.txt]
 |
+microgravity/transcript profiling
 |
-E-GEOD-39607
+/22/13
 |
 |
-|
- JD: skipped it
 |
@@ Line 347: / Line 428: @@
 |-
 |
+Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli
+|
+PMID:22869698<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3427108/ pnas]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM540098 GSM540098]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21652/ E-GEOD-21652]
 |
+loaded 07/10/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21652.idf.txt E-GEOD-21652.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21652.sdrf.txt E-GEOD-21652.sdrf.txt]
+needs c3-4
 |
-E-GEOD-30679
+Biotechnology/Transcript profiling
 |
+/22/13
 |
@@ Line 368: / Line 463: @@
 |-
 |
+Global transcriptional response of E. coli to the presence and absence of bile salts
 |
+no publication
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20380 GSE20380]
 |
-E-GEOD-30692
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-20380/ E-GEOD-20380]
 |
+loaded 07/15/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-20380.idf.txt E-GEOD-20380.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-20380.sdrf.txt E-GEOD-20380.sdrf.txt]
+ready to load?
 |
+bile acids/transcript profiling
 |
+/22/13
-|-
 |
@@ Line 395: / Line 494: @@
 |
+|-
 |
-E-GEOD-30424
+Expression data from QdNOs treated Escherichia coli
 |
+no publication
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39607 GSE39607]
 |
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-39607/ E-GEOD-39607]
 |
+loaded 07/15/13
-|-
-|
-|
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-39607.idf.txt E-GEOD-39607.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-39607.sdrf.txt E-GEOD-39607.sdrf.txt]
+needs c4
 |
-E-GEOD-34046
+Antimicrobial agent/transcript profiling
 |
+/22/13
 |
@@ Line 431: / Line 531: @@
 |-
 |
+Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression
 |
+PMID:23106382<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/1574-6968.12035/full fmes-micro]
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM760801 GSM760801]
 |
-E-GEOD-21857
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30679/ E-GEOD-30679]
 |
+loaded 5/26/13
 |
+/24/13 - DAS
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30679.idf.txt E-GEOD-30679.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30679.sdrf.txt E-GEOD-30679.sdrf.txt]
+needs c3-4
 |
+diglutathionylspermidine/transcription profiling
 |
+/22/13
+|
++
+|
++
+|
++
+|
+complete 05/30/13
 |-
 |
+Antitoxin DinJ influences the general stress response through transcript stabilizer CspE
+|
+PMID:22026739<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02618.x/full env_microb]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM761209 GSM761209]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30692/ E-GEOD-30692]
 |
+loaded 06/07/13
 |
+/10/13 - DAS
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30692.idf.txt E-GEOD-30692.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30692.sdrf.txt E-GEOD-30692.sdrf.txt]
+needs c3
 |
-E-TABM-86
+Toxin-antitoxin system/Stress response
 |
+/22/13
 |
++
 |
++
 |
++
 |
+complete 07/10/13
 |-
 |
+Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation.
+|
+PMID:22274708<br/>
+[http://link.springer.com/article/10.1007/s00253-012-3881-y/fulltext.html AMB]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30424 GSE30424]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30424/ E-GEOD-30424]
 |
+loaded 07/03/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30424.idf.txt E-GEOD-30424.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30424.sdrf.txt E-GEOD-30424.sdrf.txt]
+ready to load?
 |
-E-GEOD-29803
+biofilm/Indole
 |
+/22/13
 |
@@ Line 494: / Line 636: @@
 |-
 |
+Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7
 |
+PMID:22589288<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372972/ Bio]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34046 GSE34046]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-34046/ E-GEOD-34046]
+|
+loaded 6/27/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34046.idf.txt E-GEOD-34046.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34046.sdrf.txt E-GEOD-34046.sdrf.txt]
+ready to load?
 |
-E-GEOD-40427
+virulence/Ethanolamine
 |
+/22/13
 |
@@ Line 523: / Line 679: @@
 |
-E-GEOD-33212
+E-GEOD-21857
 |
+loaded (partially, as E-GEOD-21820)
 |
 |
+JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen).
+Capture only expression data: E-GEOD-21820
 |
-|
-|-
 |
@@ Line 544: / Line 698: @@
 |
-E-GEOD-42205
+|-
 |
@@ Line 554: / Line 709: @@
 |
+E-TABM-86
-|-
 |
@@ Line 564: / Line 718: @@
 |
-|
-E-GEOD-40557
 |
@@ Line 578: / Line 730: @@
 |-
 |
+Protein acetylation in prokaryotes increases stress resistance
 |
+PMID:21703240<br/>
+[http://www.sciencedirect.com/science/article/pii/S0006291X11010497 BBRC]
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29803 GSE29803]
 |
-E-GEOD-39439
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-29803/ E-GEOD-29803]
 |
+loaded 07/10/13
 |
 |
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29803.idf.txt E-GEOD-29803.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29803.sdrf.txt E-GEOD-29803.sdrf.txt]
+needs c3-4?
 |
+Lysine acetylation/stress resistance
 |
+/25/13
-|-
 |
@@ Line 605: / Line 762: @@
 |
-|
+|-
-E-GEOD-35049
 |
@@ Line 617: / Line 773: @@
 |
+E-GEOD-40427
-|-
 |
@@ Line 627: / Line 782: @@
 |
-|
-E-GEOD-35822
 |
@@ Line 649: / Line 802: @@
 |
-E-GEOD-41093
+E-GEOD-33212
 |
@@ Line 658: / Line 811: @@
 |
-|
-|-
 |
@@ Line 670: / Line 820: @@
 |
-E-GEOD-41940
+|-
 |
@@ Line 680: / Line 831: @@
 |
+E-GEOD-42205
-|-
 |
@@ Line 690: / Line 840: @@
 |
-|
-E-GEOD-41938
 |
@@ Line 712: / Line 860: @@
 |
-E-GEOD-26223
+E-GEOD-40557
+|
+|
+|
+|
 |
@@ Line 733: / Line 889: @@
 |
-E-MTAB-996
+E-GEOD-39439
+|
+|
+|
+|
 |
@@ Line 746: / Line 910: @@
 |-
 |
-Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22331529<br/>
-http://onlinelibrary.wiley.com/doi/10.1002/bem.21709/full
 |
-Affymetrix E. coli Genome 2.0 Array
 |
-GSE35371
 |
-E-GEOD-35371
+E-GEOD-35049
 |
-in process
 |
 |
-JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt
-http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt
-<br/>
-needs c3-c4
 |
-Transcript profiling/Magnetic field
 |
-/25/13
-|-
 |
-Evolution of gene expression during long term coexistence in a bacterial evolution experiment
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22645336<br/>
-http://www.pnas.org/content/109/24/9487.long
 |
-Affymetrix E. coli Genome 2.0 Array
 |
-GSE30639
+|-
 |
-E-GEOD-30639
 |
-in process
 |
 |
-JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt<br/>
-needs c3-c4
 |
-evolution/chemostat
+E-GEOD-35822
 |
-/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<br/>
-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<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt
-|
-biofilm/urine
-|
-/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
+E-GEOD-41093
 |
-in process
 |
 |
-JD<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt
 |
-ETOH shock/rpoS
 |
-/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<br/>
-http://nar.oxfordjournals.org/content/38/5/1636.long
 |
-Affymetrix E. coli Genome 2.0 Array
 |
-GSE15406 <br/>(GSE15404, GSE15405)
+|-
 |
-E-GEOD-15406 <br/>
-(E-GEOD-15404, E-GEOD-15405)
 |
-in process
 |
 |
-JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt<br/>
-needs c1-c4
 |
-Overexpression/????
+E-GEOD-41940
 |
-/26/13
-|-
 |
-Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate
 |
-http://www.ncbi.nlm.nih.gov/pubmed/20501031<br/>
-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<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt<br/>
+|-
-http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt<br/>
-c1-c4
 |
-benzoate/??????
 |
-/26/13
-|-
 |
-E.coli response to Antimicrobial Arylamides
 |
-http://www.ncbi.nlm.nih.gov/pubmed/21844313<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195038/#B7
 |
-Affymetrix E. coli Genome 2.0 Array
+E-GEOD-41938
 |
-GSE31140
 |
-E-GEOD-31140
 |
-in process
 |
 |
-JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt<br/>
-needs c3-c4
 |
-antimicrobial agent/transcription profile
 |
-/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<br/>
+E-GEOD-26223
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt<br/>
-needs c1-c4
 |
-Salt tolerance/Radiation resistance
 |
-/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.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22008207<br/>
-http://www.mcponline.org/content/11/1/M111.009019.long
 |
-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<br/>
-http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt
- needs c3-c4
-|
-cold treatment/water activity
-|
-/27/13
 |-
 |
-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<br/>
-http://iai.asm.org/content/75/2/966.long
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array
 |
 |
-E-MEXP-926
+E-MTAB-996
 |
-in process
 |
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt
- needs c2-4
 |
-urine/biofilm
 |
-/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<br/>
-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<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt<br/>
- needs c1-c4
-|
-urine/biofilm
-|
-/27/13
 |-
 |
-Impact of cranberry on Escherichia coli cellular surface characteristics.
+Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields
 |
-http://www.ncbi.nlm.nih.gov/pubmed/18957286<br/>
+PMID:22331529
-http://www.sciencedirect.com/science/article/pii/S0006291X08020913
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE12554
+GSE35371
 |
-E-GEOD-12554
+E-GEOD-35371
 |
-in process
+loaded 6/28/13
 |
 |
- JD
+JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-35371.idf.txt]<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-35371.sdrf.txt]
- needs c3-c4
+<br/>
+needs c3-c4
 |
-antibacterial agent/cranberry juice
+Transcript profiling/Magnetic field
 |
-/27/13
+/25/13
-|-
 |
-Evolvability and hierarchy in rewired bacterial gene networks.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/18421347<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666274<br/>
-http://www.nature.com/nature/journal/v452/n7189/full/nature06847.html
-|
-Affymetrix GeneChip E.coli Genome 2.0 Array
 |
 |
-E-MEXP-732
+|-
 |
-in process
+Evolution of gene expression during long term coexistence in a bacterial evolution experiment
 |
+PMID:22645336<br/>
+[http://www.pnas.org/content/109/24/9487.long PNAS]
 |
- JD
+Affymetrix E. coli Genome 2.0 Array
-http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt<br/>
-needs c1-c4
 |
-regulatory networks/evolvability
+GSE30639
 |
-/28/13
+E-GEOD-30639
-|-
 |
-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
+loaded 6/27/13
 |
-no publication
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array
+JD<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt E-GEOD-30639.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt E-GEOD-30639.sdrf.txt]<br/>
+needs c3-c4
 |
-GSE34275
+evolution/chemostat
 |
-E-GEOD-34275
+/26/13
 |
-in process
 |
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt<br/>
- needs c1-c4
 |
-Growth medium/glycerol
-|
-/28/13
 |-
 |
-Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli
+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/22018139<br/>
+PMID:20886356<br/>
-http://www.amb-express.com/content/1/1/33
+[http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html mgg]
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array
 |
-GSE29440
 |
-E-GEOD-29440
+E-MEXP-2609
 |
-in process
+loaded 03/25/13
 |
+/20/13 - DAS
 |
- JD
+JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt E-MEXP-2609.idf.txt]<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt
+[http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt E-MEXP-2609.sdrf.txt]
- needs c1-c4
 |
-biotechnology/recombinant proteins
+biofilm/urine
 |
-/28/13
+/26/13
-|-
 |
-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.ncbi.nlm.nih.gov/pubmed/22018139<br/>http://www.amb-express.com/content/1/1/33
++
- http://www.ncbi.nlm.nih.gov/pubmed/22134216<br/>http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g
 |
-Affymetrix E. coli Genome 2.0 Array
++
 |
-GSE28412
+complete (redone 5/9/13)
+|-
 |
-E-GEOD-28412
+Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase
 |
-in process
+no publication listed
 |
+Affymetrix GeneChip E.coli Genome 2.0 Array
 |
- JD
+GSE17526
-http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt
- needs c1-c4
 |
-biotechnology/recombinant proteins
+E-GEOD-17526
 |
-/28/13
+loaded 5/14/13
-|-
 |
-Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture
+/30/2013 - DAS
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22018139<br/>
+JD<br/>
-http://www.amb-express.com/content/1/1/33
+[http://expression.porteco.org/MicroArray/data/E-GEOD-17526.idf.txt E-GEOD-17526.idf.txt]<br/>
-|
+[http://expression.porteco.org/MicroArray/data/E-GEOD-17526.sdrf.txt E-GEOD-17526.sdrf.txt]
-Affymetrix E. coli Genome 2.0 Array
-|
-GSE29439
 |
-E-GEOD-29439
+Ethanol shock/rpoS
 |
-in process
+/26/13
 |
++
 |
- JD
++
-http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt
- needs c1-c4
 |
-biotechnology/recombinant proteins
++
 |
-/28/13
+complete on 5/15/13
 |-
 |
-Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli
+Expression data from E. coli cells overexpressing GraL for short and long periods of time
 |
-no publication
+PMID:20008510
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE29486
+GSE15406 <br/>(GSE15404, GSE15405)
 |
-E-GEOD-29486
+E-GEOD-15406 <br/>
+(E-GEOD-15404, E-GEOD-15405)
 |
-in process
+loaded 6/28/13
 |
 |
- JD
+JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt E-GEOD-15406.idf.txt]<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt
+[http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt E-GEOD-15406.sdrf.txt]<br/>
- needs c1-c4
+needs c1-c4
 |
-biotechnology/recombinant proteins
+Overexpression/????
 |
-/28/13
+/26/13
-|-
 |
-Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.
-|
-http://www.ncbi.nlm.nih.gov/pubmed/23090957<br/>
-http://iai.asm.org/content/81/1/80.long
-|
-Affymetrix E. coli Genome 2.0 Array
-|
-GSE28399
-|
-E-GEOD-28399
-|
-in process
 |
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt
- needs c3-c4
- missing one cel file
 |
-UPEC/high osmolarity
-|
-/28/13
 |-
 |
-Metabolic and transcriptional response to cofactor perturbations in Escherichia coli
+Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate
 |
-http://www.ncbi.nlm.nih.gov/pubmed/20299454<br/>
+PMID:20501031
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE20374
+GSE17519
 |
-E-GEOD-20374
+E-GEOD-17519
 |
-in process
+loaded 07/11/13
 |
 |
- JD
+JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt E-GEOD-17519.idf.txt]<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt
+[http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt E-GEOD-17519.sdrf.txt]<br/>
- needs c1-c4
+c1-c4
+|
+benzoate/transcript profiling
+|
+/26/13
+|
+|
 |
-cofactor/transcriptional profiling
 |
-/28/13
 |-
 |
-Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies
+E. coli response to Antimicrobial Arylamides
 |
-http://www.ncbi.nlm.nih.gov/pubmed/?term=19806199<br/>
+PMID:21844313
-http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007316
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE14796
+GSE31140
 |
-E-GEOD-14796
+E-GEOD-31140
 |
-in process
+loaded 03/19/13
+re-loaded 04/14/13
 |
+/17/13 - DAS
+sdrf file at AE didn't have a column for Sample Name
+|
+JD<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-31140.sdrf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt E-GEOD-31140.idf.txt]<br/>
+needs c3-c4
+|
+antimicrobial agent/transcription profile
 |
- JD
+/26/13
-http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt<br/>
+|
-http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt
++
- needs c3-4
+|
++
+|
++
+|
+complete (redone 05/08/13)
+|-
+|
+Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock
 |
-L-form/transcription profiling
+[http://www.ncbi.nlm.nih.gov/sites/entrez/21380435 pmid]<br/>
+[http://pubs.rsc.org/en/content/articlehtml/2011/mb/c0mb00336k paper]
 |
-/01/13
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE17465
+|
+E-GEOD-17465
+|
+loaded 07/16/13
+|
+|
+JD<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt E-GEOD-17465.sdrf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt E-GEOD-17465.sidf.txt]<br/>
+needs c1-c4
+|
+Salt tolerance/Radiation resistance
+|
+/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.
+|
+PMID:22008207
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+E-MTAB-623
+|
+loaded 07/09/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt E-MTAB-623.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt E-MTAB-623.sdrf.txt]
+needs c3-c4
+|
+cold-shock/water activity
+|
+/27/13
+|
+|
+|
+|
+|-
+|
+Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.
+|
+PMID:17145952
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+E-MEXP-926
+|
+loaded 6/27/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt E-MEXP-926.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt E-MEXP-926.sdrf.txt]
+needs c2-4
+|
+urine/biofilm
+|
+/27/13
+|
+|
+|
+|
+|-
+|
+Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.
+|
+PMID:20444967
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+E-MEXP-2298
+|
+loaded 6/27/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt E-MEXP-2298.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt E-MEXP-2298.sdrf.txt]<br/>
+needs c1-c4
+|
+urine/biofilm
+|
+/27/13
+|
+|
+|
+|
+|-
+|
+Impact of cranberry on Escherichia coli cellular surface characteristics.
+|
+PMID:18957286
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE12554
+|
+E-GEOD-12554
+|
+loaded 07/03/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt E-GEOD-12554.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt E-GEOD-12554.sdrf.txt]
+needs c3-c4
+|
+antibacterial agent/cranberry juice
+|
+/27/13
+|
+|
+|
+|
+|-
+|
+Evolvability and hierarchy in rewired bacterial gene networks.
+|
+PMID:18421347
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+E-MEXP-732
+|
+loaded 6/28/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt<br/> E-MEXP-732.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt E-MEXP-732.sdrf.txt]<br/>
+needs c1-c4
+|
+regulatory networks/evolvability
+|
+/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
+|
+[http://www.ncbi.nlm.nih.gov/pubmed/23472115 23472115 ]
+[http://dx.plos.org/10.1371/journal.pone.0057860 plosone]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+GSE34275
+|
+E-GEOD-34275
+|
+loaded 6/25/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt E-GEOD-34275.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt E-GEOD-34275.sdrf.txt]<br/>
+needs c1-c4
+|
+Growth medium/glycerol
+|
+/28/13
+|
+|
+|
+|
+|-
+|
+Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli
+|
+PMID:22018139
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE29440
+|
+E-GEOD-29440
+|
+loaded 06/24/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt E-GEOD-29440.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt E-GEOD-29440.sdrf.txt]
+needs c1-c4
+|
+biotechnology/recombinant proteins
+|
+/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
+|
+PMID:22018139
+[http://www.amb-express.com/content/1/1/33 www.amb-express.com]
+PMID:22134216
+[http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g pubs.rsc.org]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE28412
+|
+E-GEOD-28412
+|
+loaded 06/07/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt E-GEOD-28412.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt E-GEOD-28412.sdrf.txt]
+needs c1-c4
+|
+stress/recombinant proteins
+|
+/28/13
+|
+|
+|
+|
+|-
+|
+Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture
+|
+PMID:22018139
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE29439
+|
+E-GEOD-29439
+|
+loaded 06/24/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt E-GEOD-29439.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt E-GEOD-29439.sdrf.txt]
+needs c1-c4
+|
+recombinant proteins/transcript profiling
+|
+/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
+|
+loaded 07/16/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt E-GEOD-29486.idf.txt]
+needs c1-c4
+|
+biotechnology/recombinant proteins
+|
+/28/13
+|
+|
+|
+|
+|-
+|
+Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.
+|
+PMID:23090957<br/>
+[http://iai.asm.org/content/81/1/80.long IAI]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE28399
+|
+E-GEOD-28399
+|
+loaded on 5/16/13
+|
+/3/13 - DAS
+|
+JD: '''missing one cel file'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt E-GEOD-28399.idf.txt]
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28399.sdrf.txt E-GEOD-28399.sdrf.txt]
+missing one cel file
+|
+UPEC/high osmolarity
+|
+/28/13
+|
++
+|
++  OsmolarityUPEC
+|
++
+|
+complete 5/17/13
+|-
+|
+Metabolic and transcriptional response to cofactor perturbations in Escherichia coli
+|
+PMID:20299454<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/ PMC2878514]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE20374
+|
+E-GEOD-20374
+|
+loaded 06/07/13
+|
+C1-C4 Completed AMS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt GEOD-20374.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt E-GEOD-20374.sdrf.txt]
+needs c1-c4
+|
+cofactor/transcriptional profiling
+|
+/28/13
+|
+|
+|
+|
+|-
+|
+Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies
+|
+PMID:19806199
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE14796
+|
+E-GEOD-14796
+|
+loaded 06/24/13
+|
+/08/2013 - DAS
+/09/2013 - sent to JD
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt E-GEOD-14796.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt E-GEOD-14796.sdrf.txt]
+|
+Colony/control or L-form
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete 07/10/13
+|-
+|
+Identification of genes induced on nitrate, role of OxyR
+|
+PMID:22539721<br/>
+[http://www.sciencemag.org/content/336/6080/470.long Science]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE24524
+|
+E-GEOD-24524
+|
+loaded 07/03/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt E-GEOD-24524.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt E-GEOD-24524.sdrf.txt]
+need c3-4
+|
+anaerobic growth/S-Nitrosylation
+|
+/01/13
+|
+|
+|
+|
+|-
+|
+Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM
+|
+PMID:22144490
+PMC3264324
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE33895
+|
+E-GEOD-33895
+|
+loaded 6/25/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt E-GEOD-33895.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt E-GEOD-33895.sdrf.txt]
+needs c2-c4
+|
+virulence/His kinase
+|
+/01/13
+|
+|
+|
+|
+|-
+|
+Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa
+|
+PMID:22101045
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE26931
+|
+E-GEOD-26931
+|
+data are loaded in database 03/19/13
+re-loaded 04/15/13
+|
+used annot from batch loading
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt E-GEOD-26931.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt E-GEOD-26931.sdrf.txt]
+needs c1-c4
+only loading 4 slides, the ones that are assayed on coli platform
+|
+mixed culture/transcript profiling
+|
+/01/13
+|
++ (with GSE26932)
+|
++ (with GSE26932)
+|
++ (with GSE26932)
+|
+complete (redone 5/10/13)
+|-
+|
+A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.
+|
+PMID:21169565<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/ PMC3047162]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE21551
+|
+E-GEOD-21551
+|
+loaded 03/19/13
+re-loaded 04/13/13
+|
+-11-13 - DAS (waiting to hear about strains but OK to load)
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt GEOD-21551.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt E-GEOD-21551.sdrf.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 of gene expression
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/8/13)
+|-
+|
+Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol
+|
+PMID:22936779<br/>
+PMID:22936779
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE34631
+|
+E-GEOD-34631
+|
+loaded 03/19/13
+re-loaded 04/14/13
+|
+/12/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt GEOD-34631.idf.txt] <br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt E-GEOD-34631.sdrf.txt]
+needs c3-4: done
+|
+Carbon sources/Enzyme evolution
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/7/13)
+|-
+|
+Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans
+|
+PMID:22792156 <br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/ PMC3390347]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE30441
+|
+E-GEOD-30441
+|
+loaded 5/16/13
+|
+c1-4 done, AMS
+/15/13 DAS sent idf, sdrf to JD
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt GEOD-30441.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt GEOD-30441.sdrf.txt]
+|
+Stress resistance/EtOH
+|
+/01/13
+|
++
+|
++ Ethanol-irrE
+|
++
+|
+complete 5/17/13
+|-
+|
+First insights into the unexplored two-component system YehU/YehT in Escherichia coli.
+|
+PMID:22685278<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/ PMC3416263]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+E-MTAB-984
+|
+loaded 6/27/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt E-MTAB-984.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt E-MTAB-984.sdrf.txt]
+needs c1-4
+|
+Two-component systems/?????
+|
+/01/13
+|
+|
+|
+|
+|-
+|
+Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli
+|
+PMID:22684885
+[http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full biotech_bioeng]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE35100
+|
+E-GEOD-35100
+|
+loaded 03/25/13
+re-loaded 04/13/13
+|
+/20/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt E-GEOD-35100.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt E-GEOD-35100.sdrf.txt]
+|
+Chemical effects/Mutant vs Wild-type
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/7/13)
+|-
+|
+Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine
+|
+PMID:22101045
+PMC3255741
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE)
+|
+E-GEOD-26932
+|
+data loaded 03/19/13
+re-loaded 04/15/13
+|
+used annotation from batch loading
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt E-GEOD-26932.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt E-GEOD-26932.sdrf.txt]
+needs c3-4
+use only data on E. coli platform
+|
+mixed culture/N-acetyl glucosamine
+actual in database:
+co-culture/minimal medium
+|
+/04/13
+|
++ (with GSE26931)
+|
++ (with GSE26931)
+|
++ (with GSE26931)
+|
+complete (redone 5/10/13)
+|-
+|
+Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock
+|
+PMID:23247721<br/>
+[http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g pubs.rsc.org]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE30838
+|
+E-GEOD-30838
+|
+completed, 03/18/13
+re-loaded 04/15/13
+|
+/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 E-GEOD-30838.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt E-GEOD-30838.sdrf.txt]
+needs c1-4: done
+pUC-A1501 described in PMID:19799945
+|
+glyphosate shock/transcriptional profiling
+|
+/04/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/8/13)
+|-
+|
+Relative expression profiling of ycdC knockout strain secreting HlyA protein
+|
+PMID:22505047<br/>
+[http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full full text]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE29266
+|
+E-GEOD-29266
+|
+loaded 07/10/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt E-GEOD-29266.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt E-GEOD-29266.sdrf.txt]
+needs c1-c4
+|
+biotechnology/protein secretion
+|
+/04/13
+|
+|
+|
+|
+|-
+|
+Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis
+|
+PMID:22210763<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/ PMC3294818]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE23417
+|
+E-GEOD-23417
+|
+loaded 07/15/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt E-GEOD-23417.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt E-GEOD-23417.sdrf.txt]
+needs c1-c4
+|
+persistence/Zinc metabolism
+|
+/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
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE11303
+|
+E-GEOD-11303
+|
+loaded 03/18/13
+|
+/13/2013 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt E-GEOD-11303.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt E-GEOD-11303.sdrf.txt]
+needs c3-4: done
+|
+stress/zinc or Chemical effects/zinc
+|
+/04/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/9/13)
+|-
+|
+Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol
+|
+PMID:22389366<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/ PMC3346451]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE35797
+|
+E-GEOD-35797
+|
+loaded 07/15/13
+|
+AMS c1-4 done
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt E-GEOD-35797.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt E-GEOD-35797.sdrf.txt]
+needs c3-4
+|
+Biofilms/drug treatment
+|
+/04/13
+|
+|
+|
+|
+|-
+|
+Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.
+|
+PMID:21398637<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/ PMC3141248]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE22207
+|
+E-GEOD-22207
+|
+loaded 07/03/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt E-GEOD-22207.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt E-GEOD-22207.sdrf.txt]
+needs c3-4
+|
+promoter/sigma factor
+|
+/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
+|
+PMID:21255366<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/ PMC3158428]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE21604
+|
+E-GEOD-21604
+|
+loaded 06/24/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt E-GEOD-21604.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt E-GEOD-21604.sdfr.txt]
+needs c2-4
+|
+biofilm/mutagenesis
+|
+/04/13
+|
+|
+|
+|
+|-
+|
+The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.
+|
+PMID:20855516<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/ PMC2981326]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE21893
+|
+E-GEOD-21893
+|
+loaded 07/11/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt E-GEOD-21893.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt E-GEOD-21893.sdrf.txt]
+needs c3-4
+|
+APEC/type VI secretion system
+|
+/05/13
+|
+|
+|
+|
+|-
+|
+BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type
+|
+PMID:22221537<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE34028
+|
+E-GEOD-34028
+|
+loaded 03/19/13
+re-loaded 04/14/13
+|
+/12/2013 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt E-GEOD-34028.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt E-GEOD-34028.sdrf.txt]
+needs c3-4: DAS added 3/12/2013
+|
+Persister cells/Mutant vs Wild-type
+|
+/05/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/7/13)
+|-
+|
+Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin
+|
+PMID:22221537<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full full text]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE31054
+|
+E-GEOD-31054
+|
+loaded 07/09/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt E-GEOD-31054.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt E-GEOD-31054.sdrf.txt]
+needs c3-4
+|
+Persister cells/Stress resistance
+|
+/05/13
+|
+|
+|
+|
+|-
+|
+Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm
+|
+PMID:22047137<br/>
+[http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704 full text]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE28193
+|
+E-GEOD-28193
+|
+loaded 6/28/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt E-GEOD-28193.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt E-GEOD-28193.sdrf.txt]
+needs c3-4
+|
+biofilm/honey
+|
+/05/13
+|
+|
+|
+|
+|-
+|
+The E. coli deletion mutant of the nusB gene
+|
+PMID:21873492
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
+|
+|
+E-MEXP-3335
+|
+loaded 5/15/13
+|
+/4/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt E-MEXP-3335.idf.txt]
+needs c3-4
+|
+tRNA modificaton/transcript profiling
+|
+/05/13
+|
++
+|
++
+|
++
+|
+complete 5/16/13
+|-
+|
+E. coli ygjD gene temperature sensitive mutant incubated at 37 oC
+|
+PMID:21873492<br/>
+[http://jb.asm.org/content/193/21/6075.full JB]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
+|
+|
+E-MEXP-3334
+|
+loaded 6/28/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt E-MEXP-3334.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt E-MEXP-3334.sdrf.txt]
+needs c1-4
+|
+tRNA modification/transcript profiling
+|
+/05/13
+|
+|
+|
+|
+|-
+|
+The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.
+|
+PMID:21873492<br/>
+[http://jb.asm.org/content/193/21/6075.full JB]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
+|
+|
+E-MEXP-3333
+|
+loaded 6/28/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt E-MEXP-3333.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt E-MEXP-3333.sdrf.txt]
+needs c2-4
+|
+tRNA modification/transcript profiling
+|
+/05/13
+|
+|
+|
+|
+|-
+|
+Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages
+|
+PMID:21221972<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/ PMC3158427]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE19953
+|
+E-GEOD-19953
+|
+loaded 06/06/13
+|
+C1-C4 Complete AMS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt E-GEOD-19953.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt E-GEOD-19953.sdrf.txt]
+needs c3-4
+|
+EHEC/biofilm
+|
+/05/13
+|
+|
+|
+|
+|-
+|
+An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.
+|
+PMID:20005205
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE18972
+|
+E-GEOD-18972
+|
+loaded 03/19/13
+re-loaded 04/13/13
+|
+/11/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt E-GEOD-18972.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt E-GEOD-18972.sdrf.txt]
+needs c1-4
+no cel files in ae
+|
+biofuel/glycerol
+|
+/05/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/8/13)
+|-
+|
+QseA regulation of virulence factors in EHEC
+|
+PMID:20444105<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40 PMC2936457]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE18118
+|
+E-GEOD-18118
+|
+loaded 07/10/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt E-GEOD-18118.idf.txt]
+needs c2-4
+|
+EHEC/virulence
+|
+/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
+|
+PMID:19060153<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/ PMC2632003]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE12701
+|
+E-GEOD-12701
+|
+was already loaded as part of publication: "Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae." together with E-GEOD-11932
+|
+c1-4 done, AMS
+/15/13 DAS sent idf, sdrf to JD
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt E-GEOD-12701.idf.txt]
+needs c2-4
+modified matrix file Absent->A, ...
+|
+biofilm/toxin-antitoxin system
+|
+/05/13
+|
++
+|
++
+|
++
+|
+complete
+|-
+|
+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
+|
+loaded 6/25/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt E-GEOD-44273.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt E-GEOD-44273.sdrf.txt]
+needs c1-4
+|
+persistence/transcript profiling
+|
+/06/13
+|
+|
+|
+|
+|-
+|
+Overexpression of BglJ and LeuO in Escherichia coli K12
+|
+PMID:22295907<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full full text]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+GSE34023
+|
+|
+loaded 07/08/13
+|
+|
+JD: '''dataset not in ae, idf/sdrf made from scratch'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt E-GEOD-34023.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt E-GEOD-34023.sdrf.txt]
+needs c1-4
+|
+Virulence/Regulation of gene expression
+|
+/06/13
+|
+|
+|
+|
+|-
+|
+Expression data from laboratory evolution of Escherichia coli on lactate or glycerol
+|
+PMID:16204189<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/ PMC1240078]
+|
+Ecoli_ASv2
+|
+GSE33147
+|
+E-GEOD-33147
+|
+loaded 05/14/13
+|
+C1-4 done, AMS
+sent idf, sdrf to JD on 5/13/13
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt E-GEOD-33147.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt E-GEOD-33147.sdrf.txt]
+needs c3-4
+|
+evolution/carbon source
+|
+/07/13
+|
++
+|
++
+|
++
+|
+complete
+|-
+|
+Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.
+|
+PMID:17112383<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/ PMC1664580]
+|
+Ecoli_ASv2
+|
+GSE5239
+|
+E-GEOD-5239
+|
+loaded 05/27/13
+|
+loaded 05/26/13
+|
+JD '''dataset has no cel files and only intensity values!'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt E-GEOD-5239.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt E-GEOD-5239.sdrf.txt]
+|
+plasmid/metabolism
+|
+/07/13
+|
++
+|
++
+|
+- (no cel files)
+|
+complete (5/31/13)
+|-
+|
+Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains
+|
+PMID:17768236<br/>
+[http://mic.sgmjournals.org/content/153/9/2922.long full text]
+|
+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)
+|
+loaded 06/07/13
+|
+C1-4 done, AMS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt E-GEOD-7398.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt E-GEOD-7398.sdrf.txt]
+needs c1-4
+|
+growth phase/fis
+|
+/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
+|
+in process
+|
+|
+JD: can't figure out how the experiment was done.
+[http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt E-TABM-103.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt E-TABM-103.sdrf.txt]
+|
+|
+/07/13
+|
+|
+|
+|
+|-
+|
+Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli
+|
+PMID:15705577<br/>
+[http://www.jbc.org/content/280/16/15921.long JB]
+|
+Ecoli_ASv2
+|
+GSE2037
+|
+E-GEOD-2037
+|
+loaded 6/28/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt E-GEOD-2037.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt E-GEOD-2037.sdrf.txt]
+needs c3-4
+no cel files available
+|
+carbon source/transcript profiling
+|
+/07/13
+|
+|
+|
+|
+|-
+|
+Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.
+|
+PMID:17576668<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/ PMC1935009]
+|
+Ecoli_ASv2
+|
+GSE5818
+|
+E-GEOD-5818
+|
+loaded on 5/17/13
+|
+/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)
+|
+JD: '''no cel files available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt E-GEOD-5818.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt 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)
+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
+|
+/08/13
+|
++
+|
++
+|
+no - no cel files available
+|
+complete 5/17/13
+|-
+|
+Enterobactin is required for biofilm development in reduced-genome Escherichia coli
+|
+PMID:21980953<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full full text]
+|
+Ecoli_ASv2
+|
+|
+E-MEXP-1408
+|
+loaded 05/30/13
+|
+/22/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt E-MEXP-1408.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt E-MEXP-1408.sdrf.txt]
+needs c1-4
+|
+biofilm/transcription profiling
+DAS suggests biofilm/Reduced genome
+|
+/08/13
+|
++
+|
++
+|
++
+|
+complete 05/30/13
+|-
+|
+Indole cell signaling occurs primarily at low temperatures in Escherichia coli
+|
+PMID:18528414
+|
+Ecoli_ASv2 and E_coli_2
+|
+GSE9923
+|
+E-GEOD-9923
+|
+loaded 07/03/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt E-GEOD-9923.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt E-GEOD-9923.sdrf.txt]
+needs c2-4
+|
+biofilm/indole
+|
+/08/13
+|
+|
+|
+|
+|-
+|
+Effect of RyhB Small RNA on Global Iron Use in Escherichia coli
+|
+PMID:16199566<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/ PMC1251601]
+|
+Ecoli_ASv2
+|
+GSE3105
+|
+E-GEOD-3105
+|
+loaded 5/16/13
+|
+/16/13 - DAS
+DAS sent idf, sdrf to JD 05/14/13
+|
+JD: '''no cel files available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt E-GEOD-3105.idf.txt]
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt E-GEOD-3105.sdrf.txt]
+|
+iron/non-coding RNA
+|
+/08/13
+|
++
+|
++
+|
+no: no cel files
+|
+complete 5/17/13
+|-
+|
+sigma32 over-expression in E. coli
+|
+PMID:15757896<br/>
+[http://www.jbc.org/content/280/18/17758.long JBC]
+|
+Ecoli_ASv2
+|
+GSE2140
+|
+E-GEOD-2140
+|
+loaded 05/31/13
+|
+/26/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt E-GEOD-2140.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt E-GEOD-2140.sdrf.txt]
+needs c2-4
+no cel files available
+|
+sigma factor/transcription profiling
+|
+/08/13
+|
++
+|
++
+|
+- (no cel files)
+|
+complete (5/31/13)
+|-
+|
+Temporal gene-expression in Escherichia coli K-12 biofilms
+|
+PMID:17222132<br/>
+[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full full text]
+|
+Ecoli_ASv2
+|
+GSE3905
+|
+E-GEOD-3905
+|
+loaded 07/11/13
+|
+|
+JD '''no cel file available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt E-GEOD-3905.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt E-GEOD-3905.sdrf.txt]
+needs c3-4
+|
+biofilm/transcription profiling
+|
+/08/13
+|
+|
+|
+|
+|-
+|
+Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation
+|
+PMID:20809290
+[http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html Full Text]
+|
+Ecoli_ASv2
+|
+|
+E-MEXP-1001
+|
+loaded 05/30/13
+|
+/27/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt E-MEXP-1001.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt E-MEXP-1001.sdrf.txt]
+needs c3-4
+|
+biofilm/F- phenocopy
+|
+/11/13
+|
++
+|
++
+|
++
+|
+complete (06/05/13)
+|-
+|
+Indole is an inter-species biofilm signal mediated by SdiA
+|
+PMID:17511876<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/ PMC1899176]
+|
+Ecoli_ASv2
+|
+GSE4562
+|
+E-GEOD-4562
+|
+loaded 07/03/13
+|
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt E-GEOD-4562.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-4562.sdrf.txt E-GEOD-4562.sdrf.txt]
+needs c3-4
+|
+biofilm/indole
+|
+/11/13
+|
+|
+|
+|
+|-
+|
+Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture
+|
+PMID:17557827<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/ PMC1952038]
+|
+Ecoli_ASv2
+|
+GSE9203
+|
+E-GEOD-9203
+|
+loaded 06/97/13
+|
+Created C1-C4 AMS
+|
+JD: '''no cel files available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt E-GEOD-9203.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt E-GEOD-9203.sdrf.txt]
+needs c3-4
+|
+Quorum sensing/biofilm
+|
+/11/13
+|
+|
+|
+|
+|-
+|
+YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling
+|
+PMID:16597943<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/ PMC1448992]
+|
+Ecoli_ASv2
+|
+GSE3937
+|
+E-GEOD-3937
+|
+loaded 5/26/13
+|
+/21/13 - DAS
+|
+JD: '''no cel files available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt E-GEOD-3937.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt E-GEOD-3937.sdrf.txt]
+needs c3-4
+|
+Quorum sensing/biofilm
+|
+/11/13
+|
++
+|
++
+|
+- (no cel files)
+|
+complete (05/30/13)
+|-
+|
+Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)
+|
+PMID:18309357
+[http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html The ISME Journal]
+|
+Ecoli_ASv2
+|
+GSE8706
+|
+E-GEOD-8706
+|
+loaded
+|
+C1-4 done, AMS
+/14/13: DAS sent idf/sdrf files to JD
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt E-GEOD-8706.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt E-GEOD-8706.sdrf.txt]
+needs c3-4
+|
+Quorum sensing/biofilm
+|
+/11/13
+|
++
+|
++
+|
++
+|
+complete (6/05/13)
+|-
+|
+luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling
+|
+PMID:16321939
+|
+Ecoli_ASv2
+|
+GSE9587
+|
+E-GEOD-9587
+|
+loaded 06/06/13)
+|
+C1-C4 Complete AMS
+|
+JD: '''one cel file is corrupted - GSM242209 - had to use chp files given'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt E-GEOD-9587.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt 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. The other dataset is E-GEOD-9582 and it was loaded in 2010.
+|
+Quorum sensing/(Mutant/wild-type)
+|
+/12/13
+|
+|
+|
+|
+|-
+|
+Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli
+|
+PMID:18790864<br/>
+[http://jb.asm.org/content/190/22/7479.full JB]
+|
+Ecoli_ASv2
+|
+|
+E-MEXP-1145
+|
+loaded 5/15/13
+|
+/03/13 - DAS
+|
+JD: E-MEXP-953 is part of same pub - already in porteco
+[http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt E-MEXP-1145.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt E-MEXP-1145.sdrf.txt]
+|
+Biofilm/F plasmid
+|
+/12/13
+|
++
+|
++
+|
++
+|
+complete 5/15/13
+|-
+|
+YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport
+|
+PMID:16385049
+|
+Ecoli_ASv2
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]
+|
+loaded 07/15/13
+|
+AMS c1-4 done
+|
+JD: '''no cel files available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt E-GEOD-3514.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt E-GEOD-3514.sdrf.txt]
+needs c3-4
+|
+Quorum sensing/biofilm
+|
+/12/13
+|
+|
+|
+|
+|-
+|
+YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity
+|
+PMID:17293424<br/>
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/ PMC1855844]
+|
+Ecoli_ASv2
+|
+GSE5904
+|
+E-GEOD-5904
+|
+loaded 07/15/13
+|
+AMS c1-4 done
+|
+JD: '''
+no cel files available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt E-GEOD-5904.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt E-GEOD-5904.sdrf.txt]
+needs c3-4
+|
+Biofilm/transcription profiling
+|
+/12/13
+|
+|
+|
+|
+|-
+|
+Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803
+|
+PMID:17521447
+|
+Ecoli_ASv2
+|
+GSE5905
+|
+E-GEOD-5905
+|
+loaded 07/08/13
+|
+|
+JD: '''no cel files available'''
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt E-GEOD-5905.idf.txt]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt E-GEOD-5905.sdrf.txt]
+needs c3-4
+|
+biofuel/biotechnology
+|
+/12/13
+|
+|
+|
+|
+|-
+|
+A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS
+|
+PMID:22941047<br/>
+[http://www.nature.com/nchembio/journal/v8/n10/full/nchembio.1062.html#supplementary-information nchembio]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36779 GSE36779]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36779/ E-GEOD-36779]
+|
+loaded 03/26/13
+re-loaded 04/12/13
+|
+/4/13 - DAS
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-36779.idf.txt E-GEOD-36779.idf.txt]
+[http://expression.porteco.org/MicroArray/data/E-GEOD-36779.sdrf.txt E-GEOD-36779.sdrf.txt]
+ready to load? - yes (4/4/13 DAS)
+|
+Toxin-antitoxin system/transcription profiling
+|
+/22/13
+|
++
+|
++
+|
++
+|
+complete (redone - 5/7/13)
+|-
+|
+Evolutionary genome engineering using a restriction–modification system
+|
+PMID:21785135
+PMC3203608
+|
+Ecoli_ASv2
+|
+GSE21869
+|
+|
+the experimental data are loaded:
+[http://expression.porteco.org/publication.shtml?q=kojima&query=Query&from=0&perpage=500 PortEco Publication]
+|
+C1-4 done, AMS
+|
+faked idf/sdrf
+|
+Evolution/Parental strain
+Evolution/Evolved strain
+Evolution/Mutant
+|
+Nov 2012
+|
++
+|
++
+|
++
+|
+complete (redone 5/10/13)
+|-
+|
+Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli
+|
+PMID:19909729
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812665/ bbrc]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18852 GSE18852]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18852 E-GEOD-18852]
+|
+reload
+|
+yes
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18852.idf.txt E-GEOD-18852.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18852.sdrf.txt E-GEOD-18852.sdrf]
+|
+persister cells/toxin-antitoxin systems
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (5/14/13)
+|-
+|
+The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli
+|
+PMID:21292161
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072601/ mol_cell]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24875 GSE24875]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-24875/ E-GEOD-24875]
+|
+reload
+|
+yes
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-24875.idf.txt E-GEOD-24875.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-24875.sdrf.txt E-GEOD-24875.sdrf]
+|
+catabolite repression/non-coding RNA
+|
+/01/13
+|
+|
+|
+|
+wasn't missing - did not need to reload
+|-
+|
+A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP
+|
+PMID:16377617
+[http://www.jbc.org/content/281/8/4802.long jbc]
+PMID:17921306
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168620/ jbact]
+|
+A-GEOD-1246.adf.txt
+A-GEOD-3051.adf.txt
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3591 GSE3591]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3591/ E-GEOD-3591]
+|
+reload
+|
+yes
+|
+ JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3591.idf.txt E-GEOD-3591.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-3591.sdrf.txt E-GEOD-3591.sdrf]
+-channel
+|
+aerobic anaerobic transition/(nitrite/nitrate)
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/9/13)
+|-
+|
+The PurR regulon in Escherichia coli K-12 MG1655
+|
+PMID:21572102
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159470/ nar]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26588 GSE26588]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26588/ E-GEOD-26588]
+|
+reload
+|
+yes
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-26588.idf.txt E-GEOD-26588.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-26588.sdrf.txt E-GEOD-26588.sdrf]
+|
+purine metabolism/transcript profiling
+OR
+Chemical effects/wild-type vs mutant
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/8/13)
+|-
+|
+Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal
+|
+PMID:21059164
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057496/ env_micro]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22057 GSE22057]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22057/ E-GEOD-22057]
+|
+reload
+|
+yes
+|
+ JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-22057.idf.txt E-GEOD-22057.sdrf]
+|
+biofilm dispersal/transcript profiling
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/8/13)
+|-
+|
+Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle]
+|
+PMID:21984790
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232842/ jbact]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30893 GSE30893]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30893/ E-GEOD-30893]
+|
+reload
+|
+yes
+|
+ JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-30893.idf.txt E-GEOD-30893.sdrf]
+|
+type III secretion system/transcript profiling
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 05/08/13)
+|-
+|
+Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle]
+|
+PMID:21930760
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232668/ infect_immun]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28144 GSE28144]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-28144/ E-GEOD-28144]
+|
+reload
+|
+yes
+|
+ JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28144.idf.txt E-GEOD-28144.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-28144.sdrf.txt E-GEOD-28144.sdrf]
+|
+biofilms/antioxidants
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/7/13)
+|-
+|
+Dynamic omics approach identifies nutrition-mediated microbial interactions.
+|
+PMID:21058740
+[http://pubs.acs.org/doi/abs/10.1021/pr100989c j_prot_res]
+|
+Affymetrix E. coli Genome 2.0 Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18474 GSE18474]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-18474/ E-GEOD-18474]
+|
+reload
+|
+yes
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18474.idf.txt E-GEOD-18474.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-18474.sdrf.txt E-GEOD-18474.sdrf]
+load only coli data
+|
+co-culture/transcript profiling
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/8/13)
+|-
+|
+Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
+|
+PMID:20105222
+[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.02147.x/full env_micro]
+|
+Affymetrix E. coli Genome 2.0 Array
+Affymetrix E. coli Antisense Genome Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14203 GSE14203]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-14203/ E-GEOD-14203]
+|
+reload - expression data only
+|
+yes
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-GEOD-14203.idf.txt E-GEOD-14203.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-GEOD-14203.sdrf.txt E-GEOD-14203.sdrf]
+two platforms - sdrf only contains data for genome 2.0 array
+|
+toxin antitoxin systems/transcript profiling
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/9/13)
+|-
+|
+Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli
+|
+PMID:21695201
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112155/ plosone]
+|
+Affymetrix GeneChip E.coli Antisense Genome Array
+|
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3191/ E-MEXP-3191]
+|
+reload
+|
+yes
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3191.idf.txt E-MEXP-3191.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3191.sdrf.txt E-MEXP-3191.sdrf]
+|
+Heat shock/critical high temperature
+|
+/01/13
+|
++
+|
++
+|
++
+|
+complete (redone 5/8/13)
+|-
+|
+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.
+|
+PMID:19240136
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]
+|
+A-MEXP-1444
+|
+|
+E-MEXP-1872
+|
+reload
+|
+yes
+|
+|
+blue-light response/two-component system
+|
+|
++
+|
++
+|
++
+|
+complete (reloaded 5/14/13)
+|-
+|
+Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine
+|
+PMID:22753377
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418751/ iai]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-584/ E-MEXP-584]
+|
+reload
+|
+yes
+|
+JD
+[http://expression.porteco.org/MicroArray/data/E-MEXP-584.idf.txt E-MEXP-584.idf]<br/>
+[http://expression.porteco.org/MicroArray/data/E-MEXP-584.sdrf.txt E-MEXP-584.sdrf]
+|
+Asymptomatic Bacteriuria/transcription profiling
+|
+/01/13
+|
++
+|
+=
+|
++
+|
+complete (redone 5/9/13)
+|-
+|
+Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC
+|
+PMID:19240136
+[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648647/ pmc]
+|
+A-MEXP-1444
+|
+|
+E-MEXP-1877
+|
+reload
+|
+yes
+|
+|
+blue-light response/two-component system
+|
+|
++
+|
++
+|
++
+|
+complete (reloaded 5/14/13)
+|-
+|
+Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110
+|
+PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18302792 18302792]
+|
+Affymetrix E. coli Antisense Genome Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4778 GSE4778]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-4778/ E-GEOD-4778]
+|
+reloaded 6/25/13
+|
+|
+redoing this data set because there was a problem with the original loading
+|
+Stress/pH (external)
+|
+/21/2013
+|
++
+|
++
+|
++
+|
+complete 06/25/13
+|-
+|
+changes of global gene expression in E. coli during an oxygen shift
+|
+[http://www.ncbi.nlm.nih.gov/pubmed/15129285 pmid:15129285]
+[http://www.nature.com/nature/journal/v429/n6987/full/nature02456.html nature]
+|
+Affymetrix E. coli Antisense Genome Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1121 GSE1121]
+GSE1106
+GSE1107
+|
+E-GEOD-1121
+|
+reloaded 6/28/13
+|
+yes
+|
+reloaded due to error during original loading
+|
+(aerobic/anaerobic)/(mutant/wild-type)
+|
+|
++
+|
++
+|
++
+|
+/28/13
+|-
+|
+Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation
+|
+PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]
+|
+Affymetrix E. coli Antisense Genome Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6425 GSE6425]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6425/ E-GEOD-6425]
+|
+reloaded 7/02/13
+|
+yes
+|
+redoing this data set because there was a problem with the original loading
+|
+Strain comparison/(Anaerobic growth/Aerobic Growth)
+|
+|
++
+|
++
+|
++
+|
+complete 07/02/13
+|-
+|
+Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series
+|
+PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17504765 17504765]
+|
+Affymetrix E. coli Antisense Genome Array
+|
+[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6426 GSE6426]
+|
+[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-6426/ E-GEOD-6426]
+|
+reloaded 7/02/13
+|
+yes
+|
+redoing this data set because there was a problem with the original loading
+|
+Strain comparison/cecum
+|
+|
++
+|
++
+|
++
+|
+complete 07/02/13
+|-
+|
+|
+|
+|
+GSE26591
+|
+E-GEOD-26591
+|
+loaded (partially, as E-GEOD-26588)
+|
+|
+JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded
+|
+|
+|
+|
+|
+|
+|-
+|
+Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach
+|
+PMID:23536188
+[http://www.jbc.org/content/288/19/13789.full jbc]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+E-MEXP-3639
+|
+loaded 07/16/13
+|
+|
+JD:
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3639.idf.txt E-MEXP-3639.idf.txt]
+[http://expression.porteco.org/MicroArray/data/E-MEXP-3639.sdrf.txt E-MEXP-3639.sdrf.txt]
+needs c1 - c4
+|
+bleach/transcription profiling
+|
+/16/13
+|
+|
+|
+|
+|-
+|
+Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants
+|
+[http://www.ncbi.nlm.nih.gov/pubmed/23543115 pmid]<br/>
+[http://dnaresearch.oxfordjournals.org/content/20/3/263.full paper]
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+|
+E-MEXP-3811
+|
+loaded 07/16/13
+|
+|
+JD
+needs c1-4
+|
+nucleoid/transcript profiling
+|
+/16/13
+|
+|
+|
+|
+|-
+|
+Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli
+|
+[http://www.ncbi.nlm.nih.gov/pubmed/?term=18528414 pmid]<br/>
+[http://www.nature.com/ismej/journal/v2/n10/full/ismej200854a.html paper]
+|
+Affymetrix GeneChip E.coli Antisense Genome Array<br/>
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+GSE9923
+|
+E-GEOD-9923
+|
+loaded (partially)
+|
+|
+JD: '''4 slides from antisense platform are not loaded'''
+|
+|
+|
+|
+|
+|
+|-
+|
+Enterohemorrhagic Escherichia coli (EHEC) 86-24 double deletions of kdpE and cra grown in DMEM
+|
+PMID:23524613
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+GSE43659
+|
+E-GEOD-43659
+|
+loaded 07/16/13
+|
+/23/13 - DAS updated idf,sdrf
+|
+JD: needs c1-c4
+|
+virulence/transcript profiling
+|
+/16/13
+|
++
+|
++
+|
++
+|
+/23/13
+|-
+|
+Expression data from Avian Pathogenic Escherichia coli
+|
+not published
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+GSE48015
+|
+E-GEOD-48015
+|
+loaded 07/17/13
+|
+|
+|
+APEC/transcript profiling
+|
+/17/13
+|
+|
+|
+|
+|-
+|
+Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482
+|
+not published
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+GSE47418
+|
+E-GEOD-47418
+|
+loaded 07/17/13
+|
+|
+|
+EHEC/co-culture
+|
+/17/13
+|
+|
+|
+|
+|-
+|
+Expression profiling of wt and ydcR mutant strains
+|
+not published
+|
+E. coli Genome 2.0 Array
+|
+GSE48776
+|
+not yet in AE
+|
+in process
+|
+|
+JD: wait for mage_tab files<br/>
+This is part of a superset: GSE48832, which also includes hts dataset GSE48829.
+|
+|
+|
+|
+|
+|
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PortEco Microarray Pipeline: Difference between revisions

Latest revision as of 21:36, 31 July 2013

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