PortEco Microarray Pipeline: Difference between revisions

Revision as of 00:47, 16 March 2013

Title/Dataset Description	Reference	Platform	GEO Accession	ArrayExpress Accession	Data loaded	Curation completed	Notes	category/subcat	date started
Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions				E-MEXP-3800			JD: skipped it
				E-MEXP-3799			JD: skipped it
				E-GEOD-43325			JD: skipped it
				E-GEOD-29076			JD: skipped it
				E-GEOD-42702			JD: skipped it
				E-GEOD-34991			JD: skipped it
				E-GEOD-37026			JD: skipped it
				E-MTAB-1347			JD: skipped it
				E-GEOD-21820			JD: skipped it
				E-GEOD-22285			JD: skipped
				E-GEOD-40693			JD: skipped it
				E-GEOD-40648			JD: skipped it
				E-GEOD-21652			JD: skipped it
				E-GEOD-20380			JD: skipped it
				E-GEOD-39607			JD: skipped it
				E-GEOD-30679			JD: skipped it
				E-GEOD-30692			JD: skipped it
				E-GEOD-30424			JD: skipped it
				E-GEOD-34046			JD: skipped it
				E-GEOD-21857			JD: skipped it
				E-TABM-86
				E-GEOD-29803			JD: skipped it
				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^[1]	Affymetrix E. coli Genome 2.0 Array	GSE35371	E-GEOD-35371	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt needs c3-c4	Transcript profiling/Magnetic field	02/25/13
Evolution of gene expression during long term coexistence in a bacterial evolution experiment	http://www.ncbi.nlm.nih.gov/pubmed/22645336 http://www.pnas.org/content/109/24/9487.long	Affymetrix E. coli Genome 2.0 Array	GSE30639	E-GEOD-30639	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt needs c3-c4	evolution/chemostat	02/26/13
Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine.	http://www.ncbi.nlm.nih.gov/pubmed/20886356 http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-2609	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt	biofilm/urine	02/26/13
Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase	no publication	Affymetrix GeneChip E.coli Genome 2.0 Array	GSE17526	E-GEOD-17526	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt	ETOH shock/rpoS	02/26/13
Expression data from E. coli cells overexpressing GraL for short and long periods of time	PMID:20008510^[2]	Affymetrix E. coli Genome 2.0 Array	GSE15406 (GSE15404, GSE15405)	E-GEOD-15406 (E-GEOD-15404, E-GEOD-15405)	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt needs c1-c4	Overexpression/????	02/26/13
Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate	PMID:20501031^[3]	Affymetrix E. coli Genome 2.0 Array	GSE17519	E-GEOD-17519	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt c1-c4	benzoate/??????	02/26/13
E.coli response to Antimicrobial Arylamides	PMID:21844313^[4]	Affymetrix E. coli Genome 2.0 Array	GSE31140	E-GEOD-31140	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt needs c3-c4	antimicrobial agent/transcription profile	02/26/13
Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock	http://globethesis.com/?t=1100360275976128	Affymetrix E. coli Genome 2.0 Array	GSE17465	E-GEOD-17465	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt needs c1-c4	Salt tolerance/Radiation resistance	02/26/13
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^[5]	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 http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt needs c3-c4	cold treatment/water activity	02/27/13
Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.	PMID:17145952^[6]	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-926	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt needs c2-4	urine/biofilm	02/27/13
Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.	PMID:20444967^[7]	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-2298	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt needs c1-c4	urine/biofilm	02/27/13
Impact of cranberry on Escherichia coli cellular surface characteristics.	PMID:18957286^[8]	Affymetrix E. coli Genome 2.0 Array	GSE12554	E-GEOD-12554	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt needs c3-c4	antibacterial agent/cranberry juice	02/27/13
Evolvability and hierarchy in rewired bacterial gene networks.	PMID:18421347^[9]	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MEXP-732	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt http://expression.porteco.org/MicroArray/data/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	no publication	Affymetrix GeneChip E.coli Genome 2.0 Array	GSE34275	E-GEOD-34275	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt http://expression.porteco.org/MicroArray/data/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^[10]	Affymetrix E. coli Genome 2.0 Array	GSE29440	E-GEOD-29440	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt http://expression.porteco.org/MicroArray/data/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^[10] http://www.amb-express.com/content/1/1/33 PMID:22134216^[11] http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g	Affymetrix E. coli Genome 2.0 Array	GSE28412	E-GEOD-28412	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt needs c1-c4	biotechnology/recombinant proteins	02/28/13
Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture	PMID:22018139^[10]	Affymetrix E. coli Genome 2.0 Array	GSE29439	E-GEOD-29439	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt needs c1-c4	biotechnology/recombinant proteins	02/28/13
Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli	no publication	Affymetrix E. coli Genome 2.0 Array	GSE29486	E-GEOD-29486	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt needs c1-c4	biotechnology/recombinant proteins	02/28/13
Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.	http://www.ncbi.nlm.nih.gov/pubmed/23090957 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 http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt needs c3-c4 missing one cel file	UPEC/high osmolarity	02/28/13
Metabolic and transcriptional response to cofactor perturbations in Escherichia coli	http://www.ncbi.nlm.nih.gov/pubmed/20299454 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/	Affymetrix E. coli Genome 2.0 Array	GSE20374	E-GEOD-20374	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt http://expression.porteco.org/MicroArray/data/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^[12]	Affymetrix E. coli Genome 2.0 Array	GSE14796	E-GEOD-14796	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt needs c3-4	L-form/transcription profiling	03/01/13
Identification of genes induced on nitrate, role of OxyR	http://www.ncbi.nlm.nih.gov/pubmed/22539721 http://www.sciencemag.org/content/336/6080/470.long	Affymetrix E. coli Genome 2.0 Array	GSE24524	E-GEOD-24524	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt http://expression.porteco.org/MicroArray/data/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	http://www.ncbi.nlm.nih.gov/pubmed/22144490 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264324/	Affymetrix E. coli Genome 2.0 Array	GSE33895	E-GEOD-33895	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt http://expression.porteco.org/MicroArray/data/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^[13]	Affymetrix E. coli Genome 2.0 Array	GSE26931	E-GEOD-26931	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt needs c1-c4 only loading 4 slides, the ones that are assayed on coli platform	mixed culture/transcription profiling	03/01/13
A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.	http://www.ncbi.nlm.nih.gov/pubmed/21169565 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/	Affymetrix E. coli Genome 2.0 Array	GSE21551	E-GEOD-21551	in process	03-11-13 - DAS (waiting to hear about strains but OK to load)	JD http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt http://expression.porteco.org/MicroArray/data/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	03/01/13
Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol	http://www.ncbi.nlm.nih.gov/pubmed/22936779 http://www.ncbi.nlm.nih.gov/pubmed/22936779	Affymetrix E. coli Genome 2.0 Array	GSE34631	E-GEOD-34631	in process	03/12/13 - DAS	JD http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt needs c3-4: done	carbon source/glycerol carbon source/propylene glycol	03/01/13
Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans	http://www.ncbi.nlm.nih.gov/pubmed/?term=22792156 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/	Affymetrix E. coli Genome 2.0 Array	GSE30441	E-GEOD-30441	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt needs c1-4	Stress resistance/EtOH	03/01/13
First insights into the unexplored two-component system YehU/YehT in Escherichia coli.	http://www.ncbi.nlm.nih.gov/pubmed/22685278 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/	Affymetrix GeneChip E.coli Genome 2.0 Array		E-MTAB-984	in process		JD http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt http://expression.porteco.org/MicroArray/data/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	http://www.ncbi.nlm.nih.gov/pubmed/22684885 http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full	Affymetrix E. coli Genome 2.0 Array	GSE35100	E-GEOD-35100	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt needs c1-c4	stress/??????	03/01/13
Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine	http://www.ncbi.nlm.nih.gov/pubmed/22101045 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255741/	Affymetrix E. coli Genome 2.0 Array	GSE26932	E-GEOD-26932	in process the experiments are already loaded: http://expression.porteco.org/publication.shtml?q=zere&query=Query&from=0&perpage=500		JD http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt http://expression.porteco.org/MicroArray/data/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
Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock	http://www.ncbi.nlm.nih.gov/pubmed/23247721 http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g	Affymetrix E. coli Genome 2.0 Array	GSE30838	E-GEOD-30838	in process	03/14/13 - DAS DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.	JD http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt needs c1-4: done pUC-A1501 described in PMID:19799945^[14]	glyphosate shock/transcriptional profiling	03/04/13
Relative expression profiling of ycdC knockout strain secreting HlyA protein	http://www.ncbi.nlm.nih.gov/pubmed/22505047 http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full	Affymetrix E. coli Genome 2.0 Array	GSE29266	E-GEOD-29266	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt needs c1-c4	biotechnology/protein expression	03/04/13
Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis	http://www.ncbi.nlm.nih.gov/pubmed/22210763 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/	Affymetrix E. coli Genome 2.0 Array	GSE23417	E-GEOD-23417			JD http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt http://expression.porteco.org/MicroArray/data/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)	unpublished think data were published in PMID:22196016^[15], but no accession is listed in the paper	Affymetrix E. coli Genome 2.0 Array	GSE11303	E-GEOD-11303	in process	03/13/2013 - DAS DAS wrote authors to see if this data set is the one referred to in [[PMID:2196016]]<ref name='PMID:2196016' />	JD http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt needs c3-4: done	stress/zinc or	03/04/13
Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol	http://www.ncbi.nlm.nih.gov/pubmed/22389366 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/	Affymetrix E. coli Genome 2.0 Array	GSE35797	E-GEOD-35797	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt needs c3-4	Biofilms/drug effects	03/04/13
Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.	http://www.ncbi.nlm.nih.gov/pubmed/21398637 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/	Affymetrix E. coli Genome 2.0 Array	GSE22207	E-GEOD-22207	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt http://expression.porteco.org/MicroArray/data/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	http://www.ncbi.nlm.nih.gov/pubmed/21255366 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/	Affymetrix E. coli Genome 2.0 Array	GSE21604	E-GEOD-21604	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt<r/> http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt needs c2-4 no raw data files in ae	biofilm/mutagenesis	03/04/13
The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.	http://www.ncbi.nlm.nih.gov/pubmed/20855516 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/	Affymetrix E. coli Genome 2.0 Array	GSE21893	E-GEOD-21893	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt http://expression.porteco.org/MicroArray/data/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	http://www.ncbi.nlm.nih.gov/pubmed/22221537 http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full	Affymetrix E. coli Genome 2.0 Array	GSE34028	E-GEOD-34028	in process	03/12/2013 - DAS	JD http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt needs c3-4: DAS added 3/12/2013	persistence/?????? possible subcategory: Mutant vs Wild-type	03/05/13
Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin	http://www.ncbi.nlm.nih.gov/pubmed/22221537 http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full	Affymetrix E. coli Genome 2.0 Array	GSE31054	E-GEOD-31054	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt needs c3-4	presistence/???????	03/05/13
Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm	http://www.ncbi.nlm.nih.gov/pubmed/22047137 http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704	Affymetrix E. coli Genome 2.0 Array	GSE28193	E-GEOD-28193	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt needs c3-4	biofilm/honey	03/05/13
The E. coli deletion mutant of the nusB gene	www.ncbi.nlm.nih.gov/pubmed/21873492 http://jb.asm.org/content/193/21/6075.full	Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]		E-MEXP-3335	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt needs c3-4	tRNA modificaton/transcript profiling	03/05/13
E. coli ygjD gene temperature sensitive mutant incubated at 37 oC	www.ncbi.nlm.nih.gov/pubmed/21873492 http://jb.asm.org/content/193/21/6075.full	Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]		E-MEXP-3334	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt http://expression.porteco.org/MicroArray/data/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.	www.ncbi.nlm.nih.gov/pubmed/21873492 http://jb.asm.org/content/193/21/6075.full	Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]		E-MEXP-3333	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt http://expression.porteco.org/MicroArray/data/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	http://www.ncbi.nlm.nih.gov/pubmed/21221972 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/	Affymetrix E. coli Genome 2.0 Array	GSE19953	E-GEOD-19953	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt http://expression.porteco.org/MicroArray/data/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^[16]	Affymetrix E. coli Genome 2.0 Array	GSE18972	E-GEOD-18972	in process	03/11/13 - DAS	JD http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt needs c1-4 no cel files in ae	biofuel/glycerol	03/05/13
QseA regulation of virulence factors in EHEC	http://www.ncbi.nlm.nih.gov/pubmed/20444105 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40	Affymetrix E. coli Genome 2.0 Array	GSE18118	E-GEOD-18118	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt needs c2-4	EHEC/virulence	03/05/13
Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development	http://www.ncbi.nlm.nih.gov/pubmed/19060153 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/	Affymetrix E. coli Genome 2.0 Array	GSE12701	E-GEOD-12701	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt needs c2-4 modified matrix file Absent->A, ...	biofilm/toxin-antitoxin system	03/05/13
Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)	unpublished	Affymetrix E. coli Genome 2.0 Array	GSE44273	E-GEOD-44273	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt needs c1-4	persistence/transcript profiling	03/06/13
Overexpression of BglJ and LeuO in Escherichia coli K12	http://www.ncbi.nlm.nih.gov/pubmed/22295907 http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full	Affymetrix E. coli Genome 2.0 Array	GSE34023		in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt needs c1-4 dataset not in ae, idf/sdrf made from scratch	????/??????	03/06/13
Expression data from laboratory evolution of Escherichia coli on lactate or glycerol	http://www.ncbi.nlm.nih.gov/pubmed/16204189 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/	Ecoli_ASv2	GSE33147	E-GEOD-33147	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt needs c3-4	evolution/carbon source	03/07/13
Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.	http://www.ncbi.nlm.nih.gov/pubmed/17112383 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/	Ecoli_ASv2	GSE5239	E-GEOD-5239	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt needs c1-4 dataset has no cel files	plasmid/metabolism	03/07/13
Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains	http://www.ncbi.nlm.nih.gov/pubmed/17768236 http://mic.sgmjournals.org/content/153/9/2922.long	Ecoli_ASv2	GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)	E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt needs c1-4	????/transcription profiling	03/07/13
Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media	unpublished	Ecoli_ASv2		E-TABM-103			JD: can't figure out how the experiment was done. http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt		03/07/13
Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli	http://www.ncbi.nlm.nih.gov/pubmed/15705577 http://www.jbc.org/content/280/16/15921.long	Ecoli_ASv2	GSE2037	E-GEOD-2037	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt http://expression.porteco.org/MicroArray/data/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.	http://www.ncbi.nlm.nih.gov/pubmed/17576668 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/	Ecoli_ASv2	GSE5818	E-GEOD-5818	in process	03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)	JD http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome) no cel files available flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD	flagellum/regulation	03/08/13
Enterobactin is required for biofilm development in reduced-genome Escherichia coli	http://www.ncbi.nlm.nih.gov/pubmed/21980953 http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full	Ecoli_ASv2		E-MEXP-1408	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt needs c1-4	biofilm/transcription profiling	03/08/13
Indole cell signaling occurs primarily at low temperatures in Escherichia coli	PMID:18528414^[17]	Ecoli_ASv2 and E_coli_2	GSE9923	E-GEOD-9923	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt needs c2-4	biofilm/indole	03/08/13
Effect of RyhB Small RNA on Global Iron Use in Escherichia coli	http://www.ncbi.nlm.nih.gov/pubmed/16199566 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/	Ecoli_ASv2	GSE3105	E-GEOD-3105	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt needs c2-4 no cel files available	iron/non-coding RNA	03/08/13
sigma32 over-expression in E. coli	http://www.ncbi.nlm.nih.gov/pubmed/15757896 http://www.jbc.org/content/280/18/17758.long	Ecoli_ASv2	GSE2140	E-GEOD-2140	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt needs c2-4 no cel files available	sigma factor/transcription profiling	03/08/13
Temporal gene-expression in Escherichia coli K-12 biofilms	http://www.ncbi.nlm.nih.gov/pubmed/17222132 http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full	Ecoli_ASv2	GSE3905	E-GEOD-3905	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt needs c3-4 ne cel file available	biofilm/transcription profiling	03/08/13
Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation	http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html	Ecoli_ASv2		E-MEXP-1001	in process		JD http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt needs c3-4	biofilm/F- phenocopy	03/11/13
Indole is an inter-species biofilm signal mediated by SdiA	http://www.ncbi.nlm.nih.gov/pubmed/17511876 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/	Ecoli_ASv2	GSE4562	E-GEOD-4562	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt http://expression.porteco.org/MicroArray/data/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	http://www.ncbi.nlm.nih.gov/pubmed/17557827 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/	Ecoli_ASv2	GSE9203	E-GEOD-9203	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt needs c3-4 no cel files available	Quorum sensing/biofilm	03/11/13
YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling	http://www.ncbi.nlm.nih.gov/pubmed/16597943 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/	Ecoli_ASv2	GSE3937	E-GEOD-3937	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt needs c3-4 no cel files	Quorum sensing/biofilm	03/11/13
Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)	http://www.ncbi.nlm.nih.gov/pubmed/18309357 http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html	Ecoli_ASv2	GSE8706	E-GEOD-8706	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt needs c3-4 no cel files	Quorum sensing/biofilm	03/11/13
luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling	PMID:16321939^[18]	Ecoli_ASv2	GSE9587	E-GEOD-9587	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt needs c3-4 paper talks about expts in low/high glucose, but only low glucose data are in the set.	Quorum sensing/transcription profiling	03/12/13
Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli	http://www.ncbi.nlm.nih.gov/pubmed/18790864 http://jb.asm.org/content/190/22/7479.full	Ecoli_ASv2		E-MEXP-1145	in process		JD: E-MEXP-953 is part of same pub - already in porteco http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt	Biofilm/F plasmid	03/12/13
YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport	PMID:16385049^[19]	Ecoli_ASv2	GSE3514	E-GEOD-3514	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt needs c3-4 no cel files available conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion	Quorum sensing/biofilm	03/12/13
YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity	http://www.ncbi.nlm.nih.gov/pubmed/17293424 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/	Ecoli_ASv2	GSE5904	E-GEOD-5904	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt needs c3-4 no cel files available	Biofilm/transcription profiling	03/12/13
Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803	PMID:17521447^[20]	Ecoli_ASv2	GSE5905	E-GEOD-5905	in process		JD http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt needs c3-4 ne cel files available	biofuel/biotechnology	03/12/13
				E-GEOD-36779			JD: skipped it
Evolutionary genome engineering using a restriction–modification system	http://www.ncbi.nlm.nih.gov/pubmed/21785135 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203608/	Ecoli_ASv2	GSE21869		the experimental data are loaded: http://expression.porteco.org/publication.shtml?q=kojima&query=Query&from=0&perpage=500		no idf/sdrf	Evolution/Parental strain Evolution/Evolved strain Evolution/Mutant	Nov 2012
edit table

↑ Huwiler, SG et al. (2012) Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields. Bioelectromagnetics 33 488-96 PubMed
↑ Potrykus, K et al. (2010) Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. Nucleic Acids Res. 38 1636-51 PubMed
↑ Critzer, FJ et al. (2010) Increased transcription of the phosphate-specific transport system of Escherichia coli O157:H7 after exposure to sodium benzoate. J. Food Prot. 73 819-24 PubMed
↑ Mensa, B et al. (2011) Antibacterial mechanism of action of arylamide foldamers. Antimicrob. Agents Chemother. 55 5043-53 PubMed
↑ Kocharunchitt, C et al. (2012) Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress. Mol. Cell Proteomics 11 M111.009019 PubMed
↑ Hancock, V & Klemm, P (2007) Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine. Infect. Immun. 75 966-76 PubMed
↑ Watts, RE et al. (2010) Escherichia coli isolates causing asymptomatic bacteriuria in catheterized and noncatheterized individuals possess similar virulence properties. J. Clin. Microbiol. 48 2449-58 PubMed
↑ Johnson, BJ et al. (2008) Impact of cranberry on Escherichia coli cellular surface characteristics. Biochem. Biophys. Res. Commun. 377 992-4 PubMed
↑ Isalan, M et al. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452 840-5 PubMed
↑ ^10.0 ^10.1 ^10.2 Sharma, AK et al. (2011) Comparative transcriptomic profile analysis of fed-batch cultures expressing different recombinant proteins in Escherichia coli. AMB Express 1 33 PubMed
↑ Singh, AB et al. (2012) Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon-beta in high cell density fed batch cultures using time course transcriptomic data. Mol Biosyst 8 615-28 PubMed
↑ Glover, WA et al. (2009) Insights into the molecular basis of L-form formation and survival in Escherichia coli. PLoS ONE 4 e7316 PubMed
↑ Chu, W et al. (2012) Indole production promotes Escherichia coli mixed-culture growth with Pseudomonas aeruginosa by inhibiting quorum signaling. Appl. Environ. Microbiol. 78 411-9 PubMed
↑ Li, L et al. (2009) A novel RPMXR motif among class II 5-enolpyruvylshikimate-3-phosphate synthases is required for enzymatic activity and glyphosate resistance. J. Biotechnol. 144 330-6 PubMed
↑ Hensley, MP et al. (2012) Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli. J. Inorg. Biochem. 111 164-72 PubMed
↑ Hu, H & Wood, TK (2010) An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol. Biochem. Biophys. Res. Commun. 391 1033-8 PubMed
↑ Lee, J et al. (2008) Indole cell signaling occurs primarily at low temperatures in Escherichia coli. ISME J 2 1007-23 PubMed
↑ Wang, L et al. (2005) luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling. J. Bacteriol. 187 8350-60 PubMed
↑ Herzberg, M et al. (2006) YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. J. Bacteriol. 188 587-98 PubMed
↑ Maeda, T et al. (2007) Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803. BMC Biotechnol. 7 25 PubMed

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

[PMID:22331529-1] 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

[PMID:20008510-2] 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

[PMID:20501031-3] 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

[PMID:21844313-4] Mensa, B et al. (2011) Antibacterial mechanism of action of arylamide foldamers. Antimicrob. Agents Chemother. 55 5043-53 PubMed

[PMID:22008207-5] 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

[PMID:17145952-6] 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

[PMID:20444967-7] 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

[PMID:18957286-8] Johnson, BJ et al. (2008) Impact of cranberry on Escherichia coli cellular surface characteristics. Biochem. Biophys. Res. Commun. 377 992-4 PubMed

[PMID:18421347-9] Isalan, M et al. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452 840-5 PubMed

[PMID:22018139-10] 10.0 ^10.1 ^10.2 Sharma, AK et al. (2011) Comparative transcriptomic profile analysis of fed-batch cultures expressing different recombinant proteins in Escherichia coli. AMB Express 1 33 PubMed

[PMID:22134216-11] 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

[PMID:19806199-12] Glover, WA et al. (2009) Insights into the molecular basis of L-form formation and survival in Escherichia coli. PLoS ONE 4 e7316 PubMed

[PMID:22101045-13] 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

[PMID:19799945-14] 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

[PMID:22196016-15] 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

[PMID:20005205-16] 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

[PMID:18528414-17] Lee, J et al. (2008) Indole cell signaling occurs primarily at low temperatures in Escherichia coli. ISME J 2 1007-23 PubMed

[PMID:16321939-18] 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

[PMID:16385049-19] 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

[PMID:17521447-20] 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

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+E-GEOD-40557
 |
@@ Line 574: / Line 703: @@
 |
-|
-|-
 |
@@ Line 584: / Line 710: @@
 |
-|
+|-
-E-GEOD-35049
 |
@@ Line 596: / Line 721: @@
 |
+E-GEOD-39439
-|-
 |
@@ Line 604: / Line 728: @@
 |
-|
-|
-E-GEOD-35822
 |
@@ Line 628: / Line 748: @@
 |
-E-GEOD-41093
+E-GEOD-35049
 |
@@ Line 637: / Line 757: @@
 |
-|
-|-
 |
@@ Line 647: / Line 764: @@
 |
-|
+|-
-E-GEOD-41940
 |
@@ Line 659: / Line 775: @@
 |
+E-GEOD-35822
-|-
-|
 |
@@ Line 669: / Line 782: @@
 |
-|
-E-GEOD-41938
 |
@@ Line 691: / Line 802: @@
 |
-E-GEOD-26223
+E-GEOD-41093
+|
+|
+|
 |
@@ Line 712: / Line 829: @@
 |
-E-MTAB-996
+E-GEOD-41940
+|
+|
+|
 |
@@ Line 725: / Line 848: @@
 |-
 |
-Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields
 |
-PMID:22331529
 |
-Affymetrix E. coli Genome 2.0 Array
 |
-GSE35371
 |
-E-GEOD-35371
+E-GEOD-41938
 |
-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/>
+E-GEOD-26223
-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
 |
-/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
+E-MTAB-996
 |
-no publication
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array
 |
-GSE17526
 |
-E-GEOD-17526
 |
-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
+Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields
 |
-PMID:20008510
+PMID:22331529
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE15406 <br/>(GSE15404, GSE15405)
+GSE35371
 |
-E-GEOD-15406 <br/>
+E-GEOD-35371
-(E-GEOD-15404, E-GEOD-15405)
 |
 in process
@@ Line 838: / Line 944: @@
 |
 JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt
-http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt
-needs c1-c4
+<br/>
+needs c3-c4
+|
+Transcript profiling/Magnetic field
+|
+/25/13
+|
 |
-Overexpression/????
 |
-/26/13
 |-
 |
-Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate
+Evolution of gene expression during long term coexistence in a bacterial evolution experiment
 |
-PMID:20501031
+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
 |
-GSE17519
+GSE30639
 |
-E-GEOD-17519
+E-GEOD-30639
 |
 in process
@@ Line 863: / Line 976: @@
 |
 JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-35371.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-35371.sdrf.txt<br/>
-c1-c4
+needs c3-c4
 |
-benzoate/??????
+evolution/chemostat
 |
 /26/13
-|-
 |
-E.coli response to Antimicrobial Arylamides
+|
+|
+|-
+|
+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:21844313
+http://www.ncbi.nlm.nih.gov/pubmed/20886356<br/>
+http://link.springer.com/article/10.1007/s00438-010-0578-8/fulltext.html
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array
 |
-GSE31140
 |
-E-GEOD-31140
+E-MEXP-2609
 |
 in process
@@ Line 887: / Line 1,007: @@
 |
 JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt
-needs c3-c4
 |
-antimicrobial agent/transcription profile
+biofilm/urine
 |
 /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
+Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase
 |
-E-GEOD-17465
+no publication
+|
+Affymetrix GeneChip E.coli Genome 2.0 Array
+|
+GSE17526
+|
+E-GEOD-17526
 |
 in process
@@ Line 911: / Line 1,036: @@
 |
 JD<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-2609.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sidf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-2609.sdrf.txt
-needs c1-c4
+|
+ETOH shock/rpoS
+|
+/26/13
+|
 |
-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.
+Expression data from E. coli cells overexpressing GraL for short and long periods of time
 |
-PMID:22008207
+PMID:20008510
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array
+Affymetrix E. coli Genome 2.0 Array
 |
+GSE15406 <br/>(GSE15404, GSE15405)
 |
-E-MTAB-623
+E-GEOD-15406 <br/>
+(E-GEOD-15404, E-GEOD-15405)
 |
 in process
@@ Line 935: / Line 1,065: @@
 |
- JD
+JD<br/>
-http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-15406.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-15406.sdrf.txt<br/>
+needs c1-c4
+|
+Overexpression/????
+|
+/26/13
+|
-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.
+Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate
 |
-PMID:17145952
+PMID:20501031
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array
+Affymetrix E. coli Genome 2.0 Array
 |
+GSE17519
 |
-E-MEXP-926
+E-GEOD-17519
 |
 in process
@@ Line 960: / Line 1,096: @@
 |
- JD
+JD<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-17519.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-17519.sdrf.txt<br/>
+c1-c4
-needs c2-4
 |
-urine/biofilm
+benzoate/??????
 |
-/27/13
+/26/13
+|
+|
+|
 |-
 |
-Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.
+E.coli response to Antimicrobial Arylamides
 |
-PMID:20444967
+PMID:21844313
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array
+Affymetrix E. coli Genome 2.0 Array
 |
+GSE31140
 |
-E-MEXP-2298
+E-GEOD-31140
 |
 in process
@@ Line 985: / Line 1,126: @@
 |
-JD
+JD<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-31140.sdrf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-31140.idf.txt<br/>
+needs c3-c4
-needs c1-c4
 |
-urine/biofilm
+antimicrobial agent/transcription profile
 |
-/27/13
+/26/13
-|-
 |
-Impact of cranberry on Escherichia coli cellular surface characteristics.
 |
-PMID:18957286
 |
-Affymetrix E. coli Genome 2.0 Array
+|-
 |
-GSE12554
+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-12554
+E-GEOD-17465
 |
 in process
@@ Line 1,011: / Line 1,156: @@
 |
-JD
+JD<br/>
+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
+|
-http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt<br/>
+|
-http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt
-needs c3-c4
 |
-antibacterial agent/cranberry juice
-|
-/27/13
 |-
 |
-Evolvability and hierarchy in rewired bacterial gene networks.
+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:18421347
+PMID:22008207
 |
 Affymetrix GeneChip E.coli Genome 2.0 Array
@@ Line 1,031: / Line 1,181: @@
 |
-E-MEXP-732
+E-MTAB-623
 |
 in process
@@ Line 1,038: / Line 1,188: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MTAB-623.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MTAB-623.sdrf.txt
-needs c1-c4
+needs c3-c4
+|
+cold treatment/water activity
+|
+/27/13
+|
 |
-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
+Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.
 |
-no publication
+PMID:17145952
 |
 Affymetrix GeneChip E.coli Genome 2.0 Array
 |
-GSE34275
 |
-E-GEOD-34275
+E-MEXP-926
 |
 in process
@@ Line 1,062: / Line 1,219: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-926.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-926.sdrf.txt
- needs c1-c4
+needs c2-4
 |
-Growth medium/glycerol
+urine/biofilm
 |
-/28/13
+/27/13
-|-
 |
-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
+|-
+|
+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
 |
-GSE29440
 |
-E-GEOD-29440
+E-MEXP-2298
 |
 in process
@@ Line 1,086: / Line 1,250: @@
 |
 JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-2298.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-MEXP-2298.sdrf.txt<br/>
 needs c1-c4
 |
-biotechnology/recombinant proteins
+urine/biofilm
+|
+/27/13
+|
+|
 |
-/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
+Impact of cranberry on Escherichia coli cellular surface characteristics.
 |
-PMID:22018139
+PMID:18957286
-http://www.amb-express.com/content/1/1/33
-PMID:22134216
-http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE28412
+GSE12554
 |
-E-GEOD-28412
+E-GEOD-12554
 |
 in process
@@ Line 1,118: / Line 1,283: @@
 JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-12554.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-12554.sdrf.txt
+needs c3-c4
+|
+antibacterial agent/cranberry juice
+|
+/27/13
+|
-needs c1-c4
 |
-biotechnology/recombinant proteins
 |
-/28/13
 |-
 |
-Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture
+Evolvability and hierarchy in rewired bacterial gene networks.
 |
-PMID:22018139
+PMID:18421347
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array
 |
-GSE29439
 |
-E-GEOD-29439
+E-MEXP-732
 |
 in process
@@ Line 1,142: / Line 1,313: @@
 |
-JD
+ JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-732.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-MEXP-732.sdrf.txt<br/>
 needs c1-c4
 |
-biotechnology/recombinant proteins
+regulatory networks/evolvability
 |
 /28/13
+|
+|
+|
 |-
 |
-Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli
+Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites
 |
 no publication
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array
 |
-GSE29486
+GSE34275
 |
-E-GEOD-29486
+E-GEOD-34275
 |
 in process
@@ Line 1,168: / Line 1,344: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-34275.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-34275.sdrf.txt<br/>
   needs c1-c4
 |
-biotechnology/recombinant proteins
+Growth medium/glycerol
+|
+/28/13
+|
+|
 |
-/28/13
 |-
 |
-Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.
+Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli
 |
-http://www.ncbi.nlm.nih.gov/pubmed/23090957<br/>
+PMID:22018139
-http://iai.asm.org/content/81/1/80.long
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE28399
+GSE29440
 |
-E-GEOD-28399
+E-GEOD-29440
 |
 in process
@@ Line 1,192: / Line 1,373: @@
 |
- JD
+JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-29440.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-29440.sdrf.txt
- needs c3-c4
+needs c1-c4
+|
+biotechnology/recombinant proteins
+|
+/28/13
+|
- missing one cel file
 |
-UPEC/high osmolarity
 |
-/28/13
 |-
 |
-Metabolic and transcriptional response to cofactor perturbations in Escherichia coli
+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/20299454<br/>
+PMID:22018139
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/
+http://www.amb-express.com/content/1/1/33
+PMID:22134216
+http://pubs.rsc.org/en/content/articlehtml/2012/mb/c1mb05414g
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE20374
+GSE28412
 |
-E-GEOD-20374
+E-GEOD-28412
 |
 in process
@@ Line 1,219: / Line 1,410: @@
 |
- JD
+JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-28412.idf.txt<br/>
- needs c1-c4
+http://expression.porteco.org/MicroArray/data/E-GEOD-28412.sdrf.txt
+needs c1-c4
+|
+biotechnology/recombinant proteins
+|
+/28/13
+|
 |
-cofactor/transcriptional profiling
 |
-/28/13
 |-
 |
-Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies
+Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture
 |
-PMID:19806199
+PMID:22018139
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE14796
+GSE29439
 |
-E-GEOD-14796
+E-GEOD-29439
 |
 in process
@@ Line 1,244: / Line 1,443: @@
 |
 JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-29439.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-29439.sdrf.txt
-http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt<br/>
+needs c1-c4
-http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt
-needs c3-4
 |
-L-form/transcription profiling
+biotechnology/recombinant proteins
 |
-/01/13
+/28/13
-|-
 |
-Identification of genes induced on nitrate, role of OxyR
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22539721<br/>
-http://www.sciencemag.org/content/336/6080/470.long
+|
+|-
+|
+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
 |
-GSE24524
+GSE29486
 |
-E-GEOD-24524
+E-GEOD-29486
 |
 in process
@@ Line 1,271: / Line 1,474: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-29486.idf.txt
-  need c3-4
+  needs c1-c4
+|
+biotechnology/recombinant proteins
+|
+/28/13
+|
 |
-anaerobic growth/S-Nitrosylation
 |
-/01/13
 |-
 |
-Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM
+Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22144490<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/23090957<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264324/
+http://iai.asm.org/content/81/1/80.long
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE33895
+GSE28399
 |
-E-GEOD-33895
+E-GEOD-28399
 |
 in process
@@ Line 1,296: / Line 1,505: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-28399.idf.txt
-  needs c2-c4
+  needs c3-c4
+ missing one cel file
+|
+UPEC/high osmolarity
+|
+/28/13
+|
 |
-virulence/His kinase
 |
-/01/13
 |-
 |
-Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa
+Metabolic and transcriptional response to cofactor perturbations in Escherichia coli
 |
-PMID:22101045
+http://www.ncbi.nlm.nih.gov/pubmed/20299454<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878514/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE26931
+GSE20374
 |
-E-GEOD-26931
+E-GEOD-20374
 |
 in process
@@ Line 1,319: / Line 1,537: @@
 |
-JD
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-20374.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-20374.sdrf.txt
-http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt
+ needs c1-c4
+|
+cofactor/transcriptional profiling
+|
+/28/13
+|
-needs c1-c4
+|
-only loading 4 slides, the ones that are assayed on coli platform
 |
-mixed culture/transcription profiling
-|
-/01/13
 |-
 |
-A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.
+Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies
 |
-http://www.ncbi.nlm.nih.gov/pubmed/21169565<br/>
+PMID:19806199
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE21551
+GSE14796
 |
-E-GEOD-21551
+E-GEOD-14796
 |
 in process
 |
--11-13 - DAS (waiting to hear about strains but OK to load)
 |
 JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-21551.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-14796.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-14796.sdrf.txt
-needs c1-4: DAS added on 03/11/13
+needs c3-4
+|
+L-form/transcription profiling
+|
+/01/13
+|
-strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used
+|
 |
-beta-methylthiolation/regulation
-|
-/01/13
 |-
 |
-Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol
+Identification of genes induced on nitrate, role of OxyR
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22936779<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22539721<br/>
-http://www.ncbi.nlm.nih.gov/pubmed/22936779
+http://www.sciencemag.org/content/336/6080/470.long
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE34631
+GSE24524
 |
-E-GEOD-34631
+E-GEOD-24524
 |
 in process
 |
-/12/13 - DAS
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-24524.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-24524.sdrf.txt
+ need c3-4
+|
+anaerobic growth/S-Nitrosylation
+|
+/01/13
 |
-JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt<br/>
+|
-http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt
-needs c3-4: done
 |
-carbon source/glycerol
-carbon source/propylene glycol
-|
-/01/13
 |-
 |
-Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans
+Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM
 |
-http://www.ncbi.nlm.nih.gov/pubmed/?term=22792156<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22144490<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264324/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE30441
+GSE33895
 |
-E-GEOD-30441
+E-GEOD-33895
 |
 in process
@@ Line 1,408: / Line 1,632: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-33895.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-33895.sdrf.txt
-  needs c1-4
+  needs c2-c4
+|
+virulence/His kinase
+|
+/01/13
+|
 |
-Stress resistance/EtOH
 |
-/01/13
 |-
 |
-First insights into the unexplored two-component system YehU/YehT in Escherichia coli.
+Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22685278<br/>
+PMID:22101045
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array
+Affymetrix E. coli Genome 2.0 Array
 |
+GSE26931
 |
-E-MTAB-984
+E-GEOD-26931
 |
 in process
@@ Line 1,432: / Line 1,661: @@
 |
- JD
+JD
-http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-26931.idf.txt<br/>
- needs c1-4
+http://expression.porteco.org/MicroArray/data/E-GEOD-26931.sdrf.txt
+needs c1-c4
+only loading 4 slides, the ones that are assayed on coli platform
+|
+mixed culture/transcription profiling
+|
+/01/13
+|
 |
-Two-component systems/?????
 |
-/01/13
 |-
 |
-Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli
+A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22684885<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/21169565<br/>
-http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3047162/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE35100
+GSE21551
 |
-E-GEOD-35100
+E-GEOD-21551
 |
 in process
+|
+-11-13 - DAS (waiting to hear about strains but OK to load)
+|
+JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-21551.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/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
+|
+/01/13
 |
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt
- needs c1-c4
-|
-stress/??????
 |
-/01/13
 |-
 |
-Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine
+Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22101045<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22936779<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255741/
+http://www.ncbi.nlm.nih.gov/pubmed/22936779
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE26932
+GSE34631
 |
-E-GEOD-26932
+E-GEOD-34631
 |
 in process
+|
+/12/13 - DAS
+|
+JD
-the experiments are already loaded: http://expression.porteco.org/publication.shtml?q=zere&query=Query&from=0&perpage=500
+http://expression.porteco.org/MicroArray/data/E-GEOD-34631.idf.txt<br/>
-|
+http://expression.porteco.org/MicroArray/data/E-GEOD-34631.sdrf.txt
+needs c3-4: done
+|
+carbon source/glycerol
+carbon source/propylene glycol
+|
+/01/13
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/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
 |-
 |
-Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock
+Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans
 |
-http://www.ncbi.nlm.nih.gov/pubmed/23247721<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/?term=22792156<br/>
-http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390347/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE30838
+GSE30441
 |
-E-GEOD-30838
+E-GEOD-30441
 |
 in process
 |
-/14/13 - DAS
-DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.
 |
-JD
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-30441.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-30441.sdrf.txt
+ needs c1-4
+|
+Stress resistance/EtOH
+|
+/01/13
+|
-http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt<br/>
+|
-http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt
-needs c1-4: done
-pUC-A1501 described in PMID:19799945
 |
-glyphosate shock/transcriptional profiling
-|
-/04/13
 |-
 |
-Relative expression profiling of ycdC knockout strain secreting HlyA protein
+First insights into the unexplored two-component system YehU/YehT in Escherichia coli.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22505047<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22685278<br/>
-http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416263/
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array
 |
-GSE29266
 |
-E-GEOD-29266
+E-MTAB-984
 |
 in process
@@ Line 1,546: / Line 1,799: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MTAB-984.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-MTAB-984.sdrf.txt
-  needs c1-c4
+  needs c1-4
 |
-biotechnology/protein expression
+Two-component systems/?????
 |
-/04/13
+/01/13
-|-
 |
-Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22210763<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/
+|
+|-
+|
+Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli
+|
+http://www.ncbi.nlm.nih.gov/pubmed/22684885<br/>
+http://onlinelibrary.wiley.com/doi/10.1002/bit.24574/full
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE23417
+GSE35100
 |
-E-GEOD-23417
+E-GEOD-35100
 |
+in process
 |
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-35100.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-35100.sdrf.txt
   needs c1-c4
 |
-persistence/Zinc metabolism
+stress/??????
 |
-/04/13
+/01/13
-|-
 |
-Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)
 |
-unpublished
-think data were published in PMID:22196016, but no accession is listed in the paper
 |
-Affymetrix E. coli Genome 2.0 Array
+|-
 |
-GSE11303
+Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine
 |
-E-GEOD-11303
+http://www.ncbi.nlm.nih.gov/pubmed/22101045<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255741/
 |
-in process
+Affymetrix E. coli Genome 2.0 Array
 |
-/13/2013 - DAS
+GSE26932
+|
+E-GEOD-26932
+|
+in process
-DAS wrote authors to see if this data set is the  one referred to in <nowiki>PMID:2196016</nowiki>
+the experiments are already loaded: http://expression.porteco.org/publication.shtml?q=zere&query=Query&from=0&perpage=500
 |
-JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt
-needs c3-4: done
 |
-stress/zinc or
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-26932.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-26932.sdrf.txt
+ needs c3-4
+ use only data on E. coli platform
 |
-/04/13
+mixed culture/N-acetyl glucosamine
-|-
+actual in database:
+co-culture/minimal medium
 |
-Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol
+/04/13
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22389366<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/
 |
-Affymetrix E. coli Genome 2.0 Array
 |
-GSE35797
+|-
 |
-E-GEOD-35797
+Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock
 |
-in process
+http://www.ncbi.nlm.nih.gov/pubmed/23247721<br/>
+http://pubs.rsc.org/en/content/articlehtml/2013/mb/c2mb25374g
 |
+Affymetrix E. coli Genome 2.0 Array
 |
- JD
+GSE30838
-http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt
- needs c3-4
 |
-Biofilms/drug effects
+E-GEOD-30838
 |
-/04/13
+in process
-|-
 |
-Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.
+/14/13 - DAS
+DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/21398637<br/>
+JD
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/
+http://expression.porteco.org/MicroArray/data/E-GEOD-30838.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-30838.sdrf.txt
+needs c1-4: done
+pUC-A1501 described in PMID:19799945
 |
-Affymetrix E. coli Genome 2.0 Array
+glyphosate shock/transcriptional profiling
 |
-GSE22207
+/04/13
 |
-E-GEOD-22207
-|
-in process
 |
 |
-  JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/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
+Relative expression profiling of ycdC knockout strain secreting HlyA protein
 |
-http://www.ncbi.nlm.nih.gov/pubmed/21255366<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22505047<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/
+http://onlinelibrary.wiley.com/doi/10.1002/btpr.1550/full
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE21604
+GSE29266
 |
-E-GEOD-21604
+E-GEOD-29266
 |
 in process
@@ Line 1,675: / Line 1,936: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt<r/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-29266.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-29266.sdrf.txt
-  needs c2-4
+  needs c1-c4
+|
+biotechnology/protein expression
+|
+/04/13
+|
- no raw data files in ae
 |
-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.
+Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis
 |
-http://www.ncbi.nlm.nih.gov/pubmed/20855516<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22210763<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294818/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE21893
+GSE23417
 |
-E-GEOD-21893
+E-GEOD-23417
 |
-in process
 |
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-23417.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-23417.sdrf.txt
-  needs c3-4
+  needs c1-c4
+|
+persistence/Zinc metabolism
+|
+/04/13
+|
 |
-APEC/type Vi secretion system
 |
-/05/13
 |-
 |
-BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type
+Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine)
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22221537<br/>
+unpublished
-http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full
+think data were published in PMID:22196016, but no accession is listed in the paper
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE34028
+GSE11303
 |
-E-GEOD-34028
+E-GEOD-11303
 |
 in process
 |
-/12/2013 - DAS
+/13/2013 - DAS
+DAS wrote authors to see if this data set is the  one referred to in <nowiki>PMID:2196016</nowiki>
 |
 JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-11303.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-11303.sdrf.txt
-needs c3-4: DAS added 3/12/2013
+needs c3-4: done
+|
+stress/zinc or
+|
+/04/13
+|
 |
-persistence/??????
-possible subcategory: Mutant vs Wild-type
 |
-/05/13
 |-
 |
-Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin
+Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22221537<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22389366<br/>
-http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3346451/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE31054
+GSE35797
 |
-E-GEOD-31054
+E-GEOD-35797
 |
 in process
@@ Line 1,758: / Line 2,033: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-35797.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-35797.sdrf.txt
   needs c3-4
 |
-presistence/???????
+Biofilms/drug effects
 |
-/05/13
+/04/13
-|-
 |
-Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm
+|
+|
+|-
+|
+Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22047137<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/21398637<br/>
-http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141248/
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE28193
+GSE22207
 |
-E-GEOD-28193
+E-GEOD-22207
 |
 in process
@@ Line 1,783: / Line 2,064: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-22207.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-22207.sdrf.txt
   needs c3-4
 |
-biofilm/honey
+promoter/sigma factor
 |
-/05/13
+/04/13
-|-
 |
-The E. coli deletion mutant of the nusB gene
-|
-www.ncbi.nlm.nih.gov/pubmed/21873492<br/>
-http://jb.asm.org/content/193/21/6075.full
-|
-Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
 |
 |
-E-MEXP-3335
+|-
 |
-in process
+Biofilm dispersal of Hha13D6 vs. Hha and biofilm formation of Hha24E9 vs. Hha in E.coli K-12 BW25113 hha mutant in LBglu at 37oC
 |
+http://www.ncbi.nlm.nih.gov/pubmed/21255366<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158428/
 |
- JD
+Affymetrix E. coli Genome 2.0 Array
-http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt
- needs c3-4
 |
-tRNA modificaton/transcript profiling
+GSE21604
 |
-/05/13
+E-GEOD-21604
-|-
 |
-E. coli ygjD gene temperature sensitive mutant incubated at 37 oC
+in process
 |
-www.ncbi.nlm.nih.gov/pubmed/21873492<br/>
-http://jb.asm.org/content/193/21/6075.full
-|
-Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
 |
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-21604.idf.txt<r/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-21604.sdfr.txt
+ needs c2-4
+ no raw data files in ae
 |
-E-MEXP-3334
+biofilm/mutagenesis
 |
-in process
+/04/13
 |
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/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.
+The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain.
 |
-www.ncbi.nlm.nih.gov/pubmed/21873492<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/20855516<br/>
-http://jb.asm.org/content/193/21/6075.full
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981326/
 |
-Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
+Affymetrix E. coli Genome 2.0 Array
 |
+GSE21893
 |
-E-MEXP-3333
+E-GEOD-21893
 |
 in process
@@ Line 1,858: / Line 2,128: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-21893.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-21893.sdrf.txt
-  needs c2-4
+  needs c3-4
+|
+APEC/type Vi secretion system
+|
+/05/13
+|
 |
-tRNA modification/transcript profiling
 |
-/05/13
 |-
 |
-Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages
+BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type
 |
-http://www.ncbi.nlm.nih.gov/pubmed/21221972<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22221537<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/
+http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE19953
+GSE34028
 |
-E-GEOD-19953
+E-GEOD-34028
 |
 in process
 |
+/12/2013 - DAS
+|
+JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-34028.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-34028.sdrf.txt
+needs c3-4: DAS added 3/12/2013
+|
+persistence/??????
+possible subcategory: Mutant vs Wild-type
 |
- JD
+/05/13
-http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt<br/>
+|
-http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt
- needs c3-4
 |
-EHEC/biofilm
 |
-/05/13
 |-
 |
-An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.
+Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin
 |
-PMID:20005205
+http://www.ncbi.nlm.nih.gov/pubmed/22221537<br/>
+http://onlinelibrary.wiley.com/doi/10.1111/j.1751-7915.2011.00327.x/full
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE18972
+GSE31054
 |
-E-GEOD-18972
+E-GEOD-31054
 |
 in process
 |
-/11/13 - DAS
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-31054.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-31054.sdrf.txt
+ needs c3-4
+|
+presistence/???????
+|
+/05/13
 |
-JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt
-needs c1-4
+|
-no cel files in ae
 |
-biofuel/glycerol
-|
-/05/13
 |-
 |
-QseA regulation of virulence factors in EHEC
+Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm
 |
-http://www.ncbi.nlm.nih.gov/pubmed/20444105<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22047137<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40
+http://www.tandfonline.com/doi/full/10.1080/08927014.2011.633704
 |
 Affymetrix E. coli Genome 2.0 Array
 |
-GSE18118
+GSE28193
 |
-E-GEOD-18118
+E-GEOD-28193
 |
 in process
@@ Line 1,935: / Line 2,227: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-28193.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-28193.sdrf.txt
-  needs c2-4
+  needs c3-4
 |
-EHEC/virulence
+biofilm/honey
 |
 /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
+|
+|
+|-
+|
+The E. coli deletion mutant of the nusB gene
 |
-http://www.ncbi.nlm.nih.gov/pubmed/19060153<br/>
+www.ncbi.nlm.nih.gov/pubmed/21873492<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/
+http://jb.asm.org/content/193/21/6075.full
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
 |
-GSE12701
 |
-E-GEOD-12701
+E-MEXP-3335
 |
 in process
@@ Line 1,960: / Line 2,258: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt
+http://expression.porteco.org/MicroArray/data/E-MEXP-3335.idf.txt
-  needs c2-4
+  needs c3-4
+|
+tRNA modificaton/transcript profiling
+|
+/05/13
+|
- modified matrix file Absent->A, ...
 |
-biofilm/toxin-antitoxin system
 |
-/05/13
 |-
 |
-Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)
+E. coli ygjD gene temperature sensitive mutant incubated at 37 oC
 |
-unpublished
+www.ncbi.nlm.nih.gov/pubmed/21873492<br/>
+http://jb.asm.org/content/193/21/6075.full
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
 |
-GSE44273
 |
-E-GEOD-44273
+E-MEXP-3334
 |
 in process
 |
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-3334.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-MEXP-3334.sdrf.txt
   needs c1-4
 |
-persistence/transcript profiling
+tRNA modification/transcript profiling
+|
+/05/13
+|
+|
 |
-/06/13
 |-
 |
-Overexpression of BglJ and LeuO in Escherichia coli K12
+The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/22295907<br/>
+www.ncbi.nlm.nih.gov/pubmed/21873492<br/>
-http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full
+http://jb.asm.org/content/193/21/6075.full
 |
-Affymetrix E. coli Genome 2.0 Array
+Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]
 |
-GSE34023
 |
+E-MEXP-3333
 |
 in process
@@ Line 2,011: / Line 2,320: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-3333.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-MEXP-3333.sdrf.txt
-  needs c1-4
+  needs c2-4
+|
+tRNA modification/transcript profiling
+|
+/05/13
+|
- dataset not in ae, idf/sdrf made from scratch
 |
-????/??????
 |
-/06/13
 |-
 |
-Expression data from laboratory evolution of Escherichia coli on lactate or glycerol
+Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages
 |
-http://www.ncbi.nlm.nih.gov/pubmed/16204189<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/21221972<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158427/
 |
-Ecoli_ASv2
+Affymetrix E. coli Genome 2.0 Array
 |
-GSE33147
+GSE19953
 |
-E-GEOD-33147
+E-GEOD-19953
 |
 in process
@@ Line 2,038: / Line 2,351: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-19953.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-19953.sdrf.txt
   needs c3-4
 |
-evolution/carbon source
+EHEC/biofilm
 |
-/07/13
+/05/13
-|-
 |
-Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/17112383<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/
+|
+|-
+|
+An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol.
+|
+PMID:20005205
 |
-Ecoli_ASv2
+Affymetrix E. coli Genome 2.0 Array
 |
-GSE5239
+GSE18972
 |
-E-GEOD-5239
+E-GEOD-18972
 |
 in process
 |
+/11/13 - DAS
+|
+JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-18972.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-18972.sdrf.txt
+needs c1-4
+no cel files in ae
+|
+biofuel/glycerol
+|
+/05/13
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt
- needs c1-4
- dataset has no cel files
 |
-plasmid/metabolism
 |
-/07/13
 |-
 |
-Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains
+QseA regulation of virulence factors in EHEC
 |
-http://www.ncbi.nlm.nih.gov/pubmed/17768236<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/20444105<br/>
-http://mic.sgmjournals.org/content/153/9/2922.long
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936457/#R40
 |
-Ecoli_ASv2
+Affymetrix E. coli Genome 2.0 Array
 |
-GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)
+GSE18118
 |
-E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)
+E-GEOD-18118
 |
 in process
@@ Line 2,090: / Line 2,415: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-18118.idf.txt
-  needs c1-4
+  needs c2-4
 |
-????/transcription profiling
+EHEC/virulence
 |
-/07/13
+/05/13
-|-
 |
-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
+|-
 |
+Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development
 |
-E-TABM-103
+http://www.ncbi.nlm.nih.gov/pubmed/19060153<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632003/
 |
+Affymetrix E. coli Genome 2.0 Array
 |
+GSE12701
+|
+E-GEOD-12701
+|
+in process
+|
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-12701.idf.txt
+ needs c2-4
+ modified matrix file Absent->A, ...
 |
- JD: can't figure out how the experiment was done.
+biofilm/toxin-antitoxin system
-http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt<br/>
+|
-http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt
+/05/13
+|
 |
 |
-/07/13
 |-
 |
-Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli
+Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates)
 |
-http://www.ncbi.nlm.nih.gov/pubmed/15705577<br/>
+unpublished
-http://www.jbc.org/content/280/16/15921.long
 |
-Ecoli_ASv2
+Affymetrix E. coli Genome 2.0 Array
 |
-GSE2037
+GSE44273
 |
-E-GEOD-2037
+E-GEOD-44273
 |
 in process
 |
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-44273.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-44273.sdrf.txt
-needs c3-4
+ needs c1-4
+|
+persistence/transcript profiling
+|
+/06/13
+|
- 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.
+Overexpression of BglJ and LeuO in Escherichia coli K12
 |
-http://www.ncbi.nlm.nih.gov/pubmed/17576668<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/22295907<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/
+http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.07993.x/full
 |
-Ecoli_ASv2
+Affymetrix E. coli Genome 2.0 Array
 |
-GSE5818
+GSE34023
 |
-E-GEOD-5818
 |
 in process
 |
-/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)
 |
-JD
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-34023.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-34023.sdrf.txt
+ needs c1-4
-http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt<br/>
+ dataset not in ae, idf/sdrf made from scratch
-http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt
+|
+????/??????
+|
+/06/13
+|
-needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)
+|
-no cel files available
-flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD
 |
-flagellum/regulation
-|
-/08/13
 |-
 |
-Enterobactin is required for biofilm development in reduced-genome Escherichia coli
+Expression data from laboratory evolution of Escherichia coli on lactate or glycerol
 |
-http://www.ncbi.nlm.nih.gov/pubmed/21980953<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/16204189<br/>
-http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240078/
 |
 Ecoli_ASv2
 |
+GSE33147
 |
-E-MEXP-1408
+E-GEOD-33147
 |
 in process
@@ Line 2,196: / Line 2,542: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-33147.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-33147.sdrf.txt
-  needs c1-4
+  needs c3-4
 |
-biofilm/transcription profiling
+evolution/carbon source
 |
-/08/13
+/07/13
-|-
 |
-Indole cell signaling occurs primarily at low temperatures in Escherichia coli
 |
-PMID:18528414
 |
-Ecoli_ASv2 and E_coli_2
+|-
+|
+Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism.
+|
+http://www.ncbi.nlm.nih.gov/pubmed/17112383<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664580/
+|
+Ecoli_ASv2
 |
-GSE9923
+GSE5239
 |
-E-GEOD-9923
+E-GEOD-5239
 |
 in process
@@ Line 2,219: / Line 2,572: @@
 |
-JD
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-5239.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-5239.sdrf.txt
+ needs c1-4
-http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt<br/>
+ dataset has no cel files
-http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt
+|
+plasmid/metabolism
+|
+/07/13
+|
-needs c2-4
 |
-biofilm/indole
 |
-/08/13
 |-
 |
-Effect of RyhB Small RNA on Global Iron Use in Escherichia coli
+Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains
 |
-http://www.ncbi.nlm.nih.gov/pubmed/16199566<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/17768236<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/
+http://mic.sgmjournals.org/content/153/9/2922.long
 |
 Ecoli_ASv2
 |
-GSE3105
+GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt)
 |
-E-GEOD-3105
+E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt)
 |
 in process
@@ Line 2,247: / Line 2,606: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-7398.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-7398.sdrf.txt
-  needs c2-4
+  needs c1-4
+|
+????/transcription profiling
+|
+/07/13
+|
- no cel files available
 |
-iron/non-coding RNA
 |
-/08/13
 |-
 |
-sigma32 over-expression in E. coli
+Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media
 |
-http://www.ncbi.nlm.nih.gov/pubmed/15757896<br/>
+unpublished
-http://www.jbc.org/content/280/18/17758.long
 |
 Ecoli_ASv2
 |
-GSE2140
 |
-E-GEOD-2140
+E-TABM-103
-|
-in process
 |
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt
- needs c2-4
- no cel files available
 |
-sigma factor/transcription profiling
+ JD: can't figure out how the experiment was done.
+http://expression.porteco.org/MicroArray/data/E-TABM-103.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-TABM-103.sdrf.txt
+|
+|
+/07/13
+|
+|
 |
-/08/13
 |-
 |
-Temporal gene-expression in Escherichia coli K-12 biofilms
+Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli
 |
-http://www.ncbi.nlm.nih.gov/pubmed/17222132<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/15705577<br/>
-http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full
+http://www.jbc.org/content/280/16/15921.long
 |
 Ecoli_ASv2
 |
-GSE3905
+GSE2037
 |
-E-GEOD-3905
+E-GEOD-2037
 |
 in process
@@ Line 2,301: / Line 2,666: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-2037.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-2037.sdrf.txt
- needs c3-4
+needs c3-4
-  ne cel file available
+  no cel files available
 |
-biofilm/transcription profiling
+carbon source/transcript profiling
 |
-/08/13
+/07/13
-|-
 |
-Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation
-|
-http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt<br/>
-http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html
-|
-Ecoli_ASv2
 |
 |
-E-MEXP-1001
-|
-in process
-|
-|
-  JD
-http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt
- needs c3-4
-|
-biofilm/F- phenocopy
-|
-/11/13
 |-
 |
-Indole is an inter-species biofilm signal mediated by SdiA
+Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli.
 |
-http://www.ncbi.nlm.nih.gov/pubmed/17511876<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/17576668<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1935009/
 |
 Ecoli_ASv2
 |
-GSE4562
+GSE5818
 |
-E-GEOD-4562
+E-GEOD-5818
 |
 in process
+|
+/11/13 - DAS (waiting to hear from authors about strain background, but OK to load)
+|
+JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-5818.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-5818.sdrf.txt
+needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome)
+no cel files available
+flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD
+|
+flagellum/regulation
+|
+/08/13
 |
 |
- JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/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
+Enterobactin is required for biofilm development in reduced-genome Escherichia coli
 |
-http://www.ncbi.nlm.nih.gov/pubmed/17557827<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/21980953<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/
+http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2011.02607.x/full
 |
 Ecoli_ASv2
 |
-GSE9203
 |
-E-GEOD-9203
+E-MEXP-1408
 |
 in process
@@ Line 2,378: / Line 2,736: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-1408.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-MEXP-1408.sdrf.txt
-  needs c3-4
+  needs c1-4
+|
+biofilm/transcription profiling
+|
+/08/13
+|
- no cel files available
 |
-Quorum sensing/biofilm
 |
-/11/13
 |-
 |
-YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling
+Indole cell signaling occurs primarily at low temperatures in Escherichia coli
 |
-http://www.ncbi.nlm.nih.gov/pubmed/16597943<br/>
+PMID:18528414
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/
 |
-Ecoli_ASv2
+Ecoli_ASv2 and E_coli_2
 |
-GSE3937
+GSE9923
 |
-E-GEOD-3937
+E-GEOD-9923
 |
 in process
@@ Line 2,404: / Line 2,765: @@
 |
- JD
+JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-9923.idf.txt<br/>
- needs c3-4
+http://expression.porteco.org/MicroArray/data/E-GEOD-9923.sdrf.txt
- no cel files
+needs c2-4
 |
-Quorum sensing/biofilm
+biofilm/indole
 |
-/11/13
+/08/13
-|-
 |
-Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)
 |
-http://www.ncbi.nlm.nih.gov/pubmed/18309357<br/>
-http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html
+|
+|-
+|
+Effect of RyhB Small RNA on Global Iron Use in Escherichia coli
+|
+http://www.ncbi.nlm.nih.gov/pubmed/16199566<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1251601/
 |
 Ecoli_ASv2
 |
-GSE8706
+GSE3105
 |
-E-GEOD-8706
+E-GEOD-3105
 |
 in process
@@ Line 2,432: / Line 2,799: @@
 |
   JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-3105.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-3105.sdrf.txt
-  needs c3-4
+  needs c2-4
+ no cel files available
+|
+iron/non-coding RNA
+|
+/08/13
+|
- no cel files
 |
-Quorum sensing/biofilm
 |
-/11/13
 |-
 |
-luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling
+sigma32 over-expression in E. coli
 |
-PMID:16321939
+http://www.ncbi.nlm.nih.gov/pubmed/15757896<br/>
+http://www.jbc.org/content/280/18/17758.long
 |
 Ecoli_ASv2
 |
-GSE9587
+GSE2140
 |
-E-GEOD-9587
+E-GEOD-2140
 |
 in process
@@ Line 2,457: / Line 2,831: @@
 |
-JD
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-2140.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-2140.sdrf.txt
+ needs c2-4
-http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt<br/>
+ no cel files available
-http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt
+|
+sigma factor/transcription profiling
+|
+/08/13
+|
-needs c3-4
+|
-paper talks about expts in low/high glucose, but only low glucose data are in the set.
 |
-Quorum sensing/transcription profiling
-|
-/12/13
 |-
 |
-Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli
+Temporal gene-expression in Escherichia coli K-12 biofilms
 |
-http://www.ncbi.nlm.nih.gov/pubmed/18790864<br/>
+http://www.ncbi.nlm.nih.gov/pubmed/17222132<br/>
-http://jb.asm.org/content/190/22/7479.full
+http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2006.01143.x/full
 |
 Ecoli_ASv2
 |
+GSE3905
 |
-E-MEXP-1145
+E-GEOD-3905
 |
 in process
@@ Line 2,486: / Line 2,864: @@
 |
-JD: E-MEXP-953 is part of same pub - already in porteco
+ JD
-http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-3905.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt
+http://expression.porteco.org/MicroArray/data/E-GEOD-3905.sdrf.txt
+ needs c3-4
+ ne cel file available
+|
+biofilm/transcription profiling
+|
+/08/13
+|
+|
+|
+|-
+|
+Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation
+|
+http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt<br/>
+http://link.springer.com/article/10.1007/s00438-010-0571-2/fulltext.html
+|
+Ecoli_ASv2
+|
+|
+E-MEXP-1001
+|
+in process
+|
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-MEXP-1001.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-1001.sdrf.txt
+ needs c3-4
+|
+biofilm/F- phenocopy
+|
+/11/13
+|
+|
+|
+|-
+|
+Indole is an inter-species biofilm signal mediated by SdiA
+|
+http://www.ncbi.nlm.nih.gov/pubmed/17511876<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899176/
+|
+Ecoli_ASv2
+|
+GSE4562
+|
+E-GEOD-4562
+|
+in process
+|
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-4562.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/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
+|
+http://www.ncbi.nlm.nih.gov/pubmed/17557827<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1952038/
+|
+Ecoli_ASv2
+|
+GSE9203
+|
+E-GEOD-9203
+|
+in process
+|
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-9203.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-9203.sdrf.txt
+ needs c3-4
+ no cel files available
+|
+Quorum sensing/biofilm
+|
+/11/13
+|
+|
+|
+|-
+|
+YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling
+|
+http://www.ncbi.nlm.nih.gov/pubmed/16597943<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448992/
+|
+Ecoli_ASv2
+|
+GSE3937
+|
+E-GEOD-3937
+|
+in process
+|
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-3937.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-3937.sdrf.txt
+ needs c3-4
+ no cel files
+|
+Quorum sensing/biofilm
+|
+/11/13
+|
+|
+|
+|-
+|
+Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)
+|
+http://www.ncbi.nlm.nih.gov/pubmed/18309357<br/>
+http://www.nature.com/ismej/journal/v2/n6/full/ismej200824a.html
+|
+Ecoli_ASv2
+|
+GSE8706
+|
+E-GEOD-8706
+|
+in process
+|
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-8706.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-8706.sdrf.txt
+ needs c3-4
+ no cel files
+|
+Quorum sensing/biofilm
+|
+/11/13
+|
+|
+|
+|-
+|
+luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling
+|
+PMID:16321939
+|
+Ecoli_ASv2
+|
+GSE9587
+|
+E-GEOD-9587
+|
+in process
+|
+|
+JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-9587.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-9587.sdrf.txt
+needs c3-4
+paper talks about expts in low/high glucose, but only low glucose data are in the set.
+|
+Quorum sensing/transcription profiling
+|
+/12/13
+|
+|
+|
+|-
+|
+Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli
+|
+http://www.ncbi.nlm.nih.gov/pubmed/18790864<br/>
+http://jb.asm.org/content/190/22/7479.full
+|
+Ecoli_ASv2
+|
+|
+E-MEXP-1145
+|
+in process
+|
+|
+JD: E-MEXP-953 is part of same pub - already in porteco
+http://expression.porteco.org/MicroArray/data/E-MEXP-1145.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-MEXP-1145.sdrf.txt
+|
+Biofilm/F plasmid
+|
+/12/13
+|
+|
+|
+|-
+|
+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]
+|
+in process
+|
+|
+JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt
+needs c3-4
+no cel files available
+conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion
+|
+Quorum sensing/biofilm
+|
+/12/13
+|
+|
+|
+|-
+|
+YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity
+|
+http://www.ncbi.nlm.nih.gov/pubmed/17293424<br/>
+http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/
+|
+Ecoli_ASv2
+|
+GSE5904
+|
+E-GEOD-5904
+|
+in process
+|
+|
+ JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt
+ needs c3-4
+ no cel files available
+|
+Biofilm/transcription profiling
+|
+/12/13
+|
 |
-Biofilm/F plasmid
 |
-/12/13
 |-
 |
-YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport
+Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803
 |
-PMID:16385049
+PMID:17521447
 |
 Ecoli_ASv2
 |
-[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3514 GSE3514]
+GSE5905
 |
-[http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-3514/ E-GEOD-3514]
+E-GEOD-5905
 |
 in process
@@ Line 2,510: / Line 3,191: @@
 |
 JD
+http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-3514.idf.txt<br/>
+http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt
-http://expression.porteco.org/MicroArray/data/E-GEOD-3514.sdrf.txt
 needs c3-4
-no cel files available
+ne cel files available
+|
+biofuel/biotechnology
+|
+/12/13
+|
-conflicting annotation in GEO: based on the the intensity of the b1601_at probeset signal, GSM81020 seems to be the deletion
 |
-Quorum sensing/biofilm
 |
-/12/13
 |-
 |
-YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity
 |
-http://www.ncbi.nlm.nih.gov/pubmed/17293424<br/>
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855844/
 |
-Ecoli_ASv2
-|
-GSE5904
-|
-E-GEOD-5904
-|
-in process
 |
 |
- JD
+E-GEOD-36779
-http://expression.porteco.org/MicroArray/data/E-GEOD-5904.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-5904.sdrf.txt
- needs c3-4
- no cel files available
-|
-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
-|
-in process
 |
 |
-JD
-http://expression.porteco.org/MicroArray/data/E-GEOD-5905.idf.txt<br/>
-http://expression.porteco.org/MicroArray/data/E-GEOD-5905.sdrf.txt
-needs c3-4
-ne cel files available
 |
-biofuel/biotechnology
+JD: skipped it
-|
-/12/13
-|-
-|
-|
 |
 |
-|
-E-GEOD-36779
 |
-|
-|
-JD: skipped it
 |
@@ Line 2,623: / Line 3,259: @@
 Evolution/Mutant
 |
 Nov 2012
+|
+|
+|
 |- class="tableEdit_footer"
-|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&page=182907&pagename={{FULLPAGENAMEE}}&type=0&template= edit table]</span> || || || || || || || || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.182907.K511aabd5a75b9&page=182907&pagename={{FULLPAGENAMEE}}&type=0&template= edit table]</span> || || || || || || || || || || || ||
 |}
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PortEco Microarray Pipeline: Difference between revisions

Revision as of 00:47, 16 March 2013

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