PortEco Microarray Pipeline
<protect>
| Title/Dataset Description | Reference | Platform | GEO Accession | ArrayExpress Accession | Data loaded | Curation completed | Notes | category/subcat | date started | geneprofile | wdk | zscore | finished |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Transcription profiling by array of differential utilization of carbon sources in Escherichia coli based on previous nutritional conditions |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
loaded 07/16/13 |
JD E-MEXP-3800.idf.txt needs c1-4 |
Media comparisons/Culturing history |
03/20/13 |
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Transcription profiling by array of Escherichia coli subjected to two different types of nutritional scenarios to investigate nutritional condition dependant differential tolerance to hydrogen peroxide stress |
no publication |
Affymetrix GeneChip E.coli Genome 2.0 Array |
loaded 07/16/13 |
JD E-MEXP-3799.idf.txt needs c1-4 |
Media comparisons/H2O2 |
03/20/13 |
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|
Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor |
no publication |
Affymetrix E. coli Genome 2.0 Array |
loaded 07/15/13 |
JD E-GEOD-43325.idf.txt needs c1-c4; new organism? O55:H7 |
Quorum sensing/virulence |
03/21/13 |
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|
Nitric oxide effect in Escherichia coli O157:H7 EDL933 |
no publication |
loaded 07/16/13 |
JD E-GEOD-29076.idf.txt needs c1-4 |
Nitric oxide/transcription profiling |
03/21/13 |
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|
Global Stress Response in a Prokaryotic Model of DJ-1-Associated Parkinsonism |
Affymetrix E. coli Genome 2.0 Array |
loaded 06/06/13 |
C1-C4 Complete AMS |
JD: no cel files and only norm intensity values
E-GEOD-42702.idf.txt needs c1-4 |
Stress response/Parkinson's disease |
03/21/13 |
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|
Fucose sensing regulates bacterial intestinal colonization |
Affymetrix E. coli Genome 2.0 Array |
loaded 6/27/13 |
JD E-GEOD-34991.idf.txt needs c1-4 |
Fucose sensing/colonization |
03/21/13 |
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|
Global transcriptional responses to the bacteriocin colicin M in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
loaded 7/01/13 |
JD E-GEOD-37026.idf.txt needs c1-4 |
colicins/transcription profiling |
03/21/13 |
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|
Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
loaded 07/02/13 |
JD E-MTAB-1347.idf.txt ready to load? |
Two-component systems/transcript profiling |
03/24/13 |
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|
Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli(expression data) |
Affymetrix E. coli Genome 2.0 Array |
loaded 06/06/13 |
C1-C4 Complete AMS |
JD E-GEOD-21820.idf.txt needs c1-4 |
Starvation/Phosphate |
03/21/13 |
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|
Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence |
Affymetrix E. coli Genome 2.0 Array |
loaded 07/02/13 |
JD E-GEOD-22285.idf.txt needs c1-4 |
Virulence/Host factors |
03/21/13 |
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|
Examination of the Genome-Wide Transcriptional Response of Escherichia coli O157:H7 to Cinnamaldehyde Exposure |
Affymetrix E. coli Genome 2.0 Array |
loaded 5/16/13 |
C1-4 done, AMS 05/15/13 DAS sent idf, sdrf to JD |
JD
E-GEOD-40693.idf.txt needs c1-4 |
Antimicrobial agent/transcription profiling |
03/21/13 |
+ |
+ Cinnamaldehyde |
+ |
complete 5/17/13 | |||
|
Effect of Simulated Microgravity on E. coli K12 MG1655 Growth and Gene Expression |
Affymetrix E. coli Genome 2.0 Array |
loaded 6/25/13 |
JD |
microgravity/transcript profiling |
03/22/13 |
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|
Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
loaded 07/10/13 |
JD E-GEOD-21652.idf.txt needs c3-4 |
Biotechnology/Transcript profiling |
03/22/13 |
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|
Global transcriptional response of E. coli to the presence and absence of bile salts |
no publication |
Affymetrix E. coli Genome 2.0 Array |
loaded 07/15/13 |
JD E-GEOD-20380.idf.txt ready to load? |
bile acids/transcript profiling |
03/22/13 |
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|
Expression data from QdNOs treated Escherichia coli |
no publication |
Affymetrix E. coli Genome 2.0 Array |
loaded 07/15/13 |
JD E-GEOD-39607.idf.txt needs c4 |
Antimicrobial agent/transcript profiling |
03/22/13 |
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|
Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression |
Affymetrix E. coli Genome 2.0 Array |
loaded 5/26/13 |
05/24/13 - DAS |
JD E-GEOD-30679.idf.txt needs c3-4 |
diglutathionylspermidine/transcription profiling |
03/22/13 |
+ |
+ |
+ |
complete 05/30/13 | |||
|
Antitoxin DinJ influences the general stress response through transcript stabilizer CspE |
Affymetrix E. coli Genome 2.0 Array |
loaded 06/07/13 |
07/10/13 - DAS |
JD E-GEOD-30692.idf.txt needs c3 |
Toxin-antitoxin system/Stress response |
03/22/13 |
+ |
+ |
+ |
complete 07/10/13 | |||
|
Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation. |
Affymetrix E. coli Genome 2.0 Array |
loaded 07/03/13 |
JD E-GEOD-30424.idf.txt ready to load? |
biofilm/Indole |
03/22/13 |
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|
Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7 |
Affymetrix E. coli Genome 2.0 Array |
loaded 6/27/13 |
JD E-GEOD-34046.idf.txt ready to load? |
virulence/Ethanolamine |
03/22/13 |
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|
E-GEOD-21857 |
loaded (partially, as E-GEOD-21820) |
JD: this dataset contains 2 set: expression + chip-chip (run on NimbleGen). Capture only expression data: E-GEOD-21820 |
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|
E-TABM-86 |
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|
Protein acetylation in prokaryotes increases stress resistance |
Affymetrix E. coli Genome 2.0 Array |
loaded 07/10/13 |
JD E-GEOD-29803.idf.txt needs c3-4? |
Lysine acetylation/stress resistance |
03/25/13 |
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|
E-GEOD-40427 |
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|
E-GEOD-33212 |
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E-GEOD-42205 |
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|
E-GEOD-40557 |
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E-GEOD-39439 |
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|
E-GEOD-35049 |
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|
E-GEOD-35822 |
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|
E-GEOD-41093 |
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|
E-GEOD-41940 |
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E-GEOD-41938 |
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|
E-GEOD-26223 |
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|
E-MTAB-996 |
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|
Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields |
Affymetrix E. coli Genome 2.0 Array |
GSE35371 |
E-GEOD-35371 |
loaded 6/28/13 |
JD |
Transcript profiling/Magnetic field |
02/25/13 |
||||||
|
Evolution of gene expression during long term coexistence in a bacterial evolution experiment |
Affymetrix E. coli Genome 2.0 Array |
GSE30639 |
E-GEOD-30639 |
loaded 6/27/13 |
JD |
evolution/chemostat |
02/26/13 |
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|
Global transcription profiling of E. coli strains CFT073, Nissle 1917 and 83972 grown exponentially in MOPS, exponentially in human urine and in biofilms in human urine. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-2609 |
loaded 03/25/13 |
03/20/13 - DAS |
biofilm/urine |
02/26/13 |
+ |
+ |
+ |
complete (redone 5/9/13) | |||
|
Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase |
no publication listed |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE17526 |
E-GEOD-17526 |
loaded 5/14/13 |
3/30/2013 - DAS |
Ethanol shock/rpoS |
02/26/13 |
+ |
+ |
+ |
complete on 5/15/13 | |
|
Expression data from E. coli cells overexpressing GraL for short and long periods of time |
Affymetrix E. coli Genome 2.0 Array |
GSE15406 |
E-GEOD-15406 |
loaded 6/28/13 |
JD |
Overexpression/???? |
02/26/13 |
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|
Transcription analysis of E. coli O157:H7 when exposed to sodium benzoate |
Affymetrix E. coli Genome 2.0 Array |
GSE17519 |
E-GEOD-17519 |
loaded 07/11/13 |
benzoate/transcript profiling |
02/26/13 |
|||||||
|
E. coli response to Antimicrobial Arylamides |
Affymetrix E. coli Genome 2.0 Array |
GSE31140 |
E-GEOD-31140 |
loaded 03/19/13 re-loaded 04/14/13 |
3/17/13 - DAS sdrf file at AE didn't have a column for Sample Name |
JD |
antimicrobial agent/transcription profile |
02/26/13 |
+ |
+ |
+ |
complete (redone 05/08/13) | |
|
Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock |
Affymetrix E. coli Genome 2.0 Array |
GSE17465 |
E-GEOD-17465 |
loaded 07/16/13 |
JD |
Salt tolerance/Radiation resistance |
02/26/13 |
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|
Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MTAB-623 |
loaded 07/09/13 |
JD E-MTAB-623.idf.txt needs c3-c4 |
cold-shock/water activity |
02/27/13 |
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|
Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-926 |
loaded 6/27/13 |
JD E-MEXP-926.idf.txt needs c2-4 |
urine/biofilm |
02/27/13 |
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|
Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-2298 |
loaded 6/27/13 |
JD E-MEXP-2298.idf.txt needs c1-c4 |
urine/biofilm |
02/27/13 |
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|
Impact of cranberry on Escherichia coli cellular surface characteristics. |
Affymetrix E. coli Genome 2.0 Array |
GSE12554 |
E-GEOD-12554 |
loaded 07/03/13 |
JD E-GEOD-12554.idf.txt needs c3-c4 |
antibacterial agent/cranberry juice |
02/27/13 |
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|
Evolvability and hierarchy in rewired bacterial gene networks. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-732 |
loaded 6/28/13 |
JD
|
regulatory networks/evolvability |
02/28/13 |
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|
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 |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE34275 |
E-GEOD-34275 |
loaded 6/25/13 |
JD E-GEOD-34275.idf.txt |
Growth medium/glycerol |
02/28/13 |
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|
Design of an improved host platform for the over expression of recombinant proteins in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
GSE29440 |
E-GEOD-29440 |
loaded 06/24/13 |
JD E-GEOD-29440.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 |
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|
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 |
Affymetrix E. coli Genome 2.0 Array |
GSE28412 |
E-GEOD-28412 |
loaded 06/07/13 |
JD E-GEOD-28412.idf.txt needs c1-c4 |
stress/recombinant proteins |
02/28/13 |
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|
Global transcriptome response of recombinant protein xylanase producing E. coli in high cell density fed batch culture |
Affymetrix E. coli Genome 2.0 Array |
GSE29439 |
E-GEOD-29439 |
loaded 06/24/13 |
JD E-GEOD-29439.idf.txt needs c1-c4 |
recombinant proteins/transcript profiling |
02/28/13 |
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|
Uncoupling growth and product formation kinetics to design improved strains for recombinant protein production in escherichia coli |
no publication |
Affymetrix E. coli Genome 2.0 Array |
GSE29486 |
E-GEOD-29486 |
loaded 07/16/13 |
JD
E-GEOD-29486.idf.txt needs c1-c4 |
biotechnology/recombinant proteins |
02/28/13 |
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|
Transcriptional responses of uropathogenic E. coli to stresses caused by sodium chloride or urea. |
Affymetrix E. coli Genome 2.0 Array |
GSE28399 |
E-GEOD-28399 |
loaded on 5/16/13 |
4/3/13 - DAS |
JD: missing one cel file missing one cel file |
UPEC/high osmolarity |
02/28/13 |
+ |
+ OsmolarityUPEC |
+ |
complete 5/17/13 | |
|
Metabolic and transcriptional response to cofactor perturbations in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
GSE20374 |
E-GEOD-20374 |
loaded 06/07/13 |
C1-C4 Completed AMS |
JD GEOD-20374.idf.txt needs c1-c4 |
cofactor/transcriptional profiling |
02/28/13 |
|||||
|
Comparison of gene expression profiles of E. coli W3110 normal colonies vs. L-form colonies |
Affymetrix E. coli Genome 2.0 Array |
GSE14796 |
E-GEOD-14796 |
loaded 06/24/13 |
07/08/2013 - DAS 07/09/2013 - sent to JD |
JD |
Colony/control or L-form |
03/01/13 |
+ |
+ |
+ |
complete 07/10/13 | |
|
Identification of genes induced on nitrate, role of OxyR |
Affymetrix E. coli Genome 2.0 Array |
GSE24524 |
E-GEOD-24524 |
loaded 07/03/13 |
JD E-GEOD-24524.idf.txt need c3-4 |
anaerobic growth/S-Nitrosylation |
03/01/13 |
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|
Enterohemorrhagic Escherichia coli (EHEC)8624 double deletions of qseC and qseE grown in DMEM |
PMC3264324 |
Affymetrix E. coli Genome 2.0 Array |
GSE33895 |
E-GEOD-33895 |
loaded 6/25/13 |
JD E-GEOD-33895.idf.txt needs c2-c4 |
virulence/His kinase |
03/01/13 |
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|
Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa |
Affymetrix E. coli Genome 2.0 Array |
GSE26931 |
E-GEOD-26931 |
data are loaded in database 03/19/13 re-loaded 04/15/13 |
used annot from batch loading |
JD E-GEOD-26931.idf.txt needs c1-c4 only loading 4 slides, the ones that are assayed on coli platform |
mixed culture/transcript profiling |
03/01/13 |
+ (with GSE26932) |
+ (with GSE26932) |
+ (with GSE26932) |
complete (redone 5/10/13) | |
|
A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. |
Affymetrix E. coli Genome 2.0 Array |
GSE21551 |
E-GEOD-21551 |
loaded 03/19/13 re-loaded 04/13/13 |
03-11-13 - DAS (waiting to hear about strains but OK to load) |
JD GEOD-21551.idf.txt
strains used are unclear (mg1655/w3110?): 03/11/13: DAS wrote corresponding author about mutant alleles used |
beta-methylthiolation/regulation of gene expression |
03/01/13 |
+ |
+ |
+ |
complete (redone 5/8/13) | |
|
Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol |
Affymetrix E. coli Genome 2.0 Array |
GSE34631 |
E-GEOD-34631 |
loaded 03/19/13 re-loaded 04/14/13 |
03/12/13 - DAS |
JD GEOD-34631.idf.txt needs c3-4: done |
Carbon sources/Enzyme evolution |
03/01/13 |
+ |
+ |
+ |
complete (redone 5/7/13) | |
|
Comparing expression profiles of E. coli strains carrying an ethanol tolerant mutant (E1) or wild type (E0) IrrE gene from D. radiodurans |
Affymetrix E. coli Genome 2.0 Array |
GSE30441 |
E-GEOD-30441 |
loaded 5/16/13 |
c1-4 done, AMS 05/15/13 DAS sent idf, sdrf to JD |
JD |
Stress resistance/EtOH |
03/01/13 |
+ |
+ Ethanol-irrE |
+ |
complete 5/17/13 | |
|
First insights into the unexplored two-component system YehU/YehT in Escherichia coli. |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MTAB-984 |
loaded 6/27/13 |
JD E-MTAB-984.idf.txt needs c1-4 |
Two-component systems/????? |
03/01/13 |
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|
Comparison of the expression profiles of furfural tolerant and wt IrrE expressed in E. coli |
Affymetrix E. coli Genome 2.0 Array |
GSE35100 |
E-GEOD-35100 |
loaded 03/25/13 re-loaded 04/13/13 |
03/20/13 - DAS |
JD E-GEOD-35100.idf.txt
|
Chemical effects/Mutant vs Wild-type |
03/01/13 |
+ |
+ |
+ |
complete (redone 5/7/13) | |
|
Mixed Culture Gene Expression of E. coli and Pseudomonas aeruginosa grown on defined media with N-acetyl glucosamine |
PMC3255741 |
Affymetrix E. coli Genome 2.0 Array |
GSE) |
E-GEOD-26932 |
data loaded 03/19/13 re-loaded 04/15/13 |
used annotation from batch loading |
JD E-GEOD-26932.idf.txt needs c3-4 use only data on E. coli platform |
mixed culture/N-acetyl glucosamine actual in database: co-culture/minimal medium |
03/04/13 |
+ (with GSE26931) |
+ (with GSE26931) |
+ (with GSE26931) |
complete (redone 5/10/13) |
|
Transcriptional profile of Escherichia coli K12 strain JM109 under 200 mM glyphosate shock |
Affymetrix E. coli Genome 2.0 Array |
GSE30838 |
E-GEOD-30838 |
completed, 03/18/13 re-loaded 04/15/13 |
03/14/13 - DAS DAS wrote Dr. Liang Li about plasmid pUC-A1501, but OK to load data as is. |
JD E-GEOD-30838.idf.txt needs c1-4: done pUC-A1501 described in PMID:19799945[40] |
glyphosate shock/transcriptional profiling |
03/04/13 |
+ |
+ |
+ |
complete (redone 5/8/13) | |
|
Relative expression profiling of ycdC knockout strain secreting HlyA protein |
Affymetrix E. coli Genome 2.0 Array |
GSE29266 |
E-GEOD-29266 |
loaded 07/10/13 |
JD E-GEOD-29266.idf.txt needs c1-c4 |
biotechnology/protein secretion |
03/04/13 |
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|
Differential expression of E.coli mar/rob/soxS triple mutant and wild type in a mouse model of pyelonephritis |
Affymetrix E. coli Genome 2.0 Array |
GSE23417 |
E-GEOD-23417 |
loaded 07/15/13 |
JD E-GEOD-23417.idf.txt needs c1-c4 |
persistence/Zinc metabolism |
03/04/13 |
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|
Transcriptional responses of Escherichia coli K-12 to the zinc chelator TPEN (N,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine) |
corresponding author confirmed that data were published in PMID:22196016[43] |
Affymetrix E. coli Genome 2.0 Array |
GSE11303 |
E-GEOD-11303 |
loaded 03/18/13 |
03/13/2013 - DAS |
JD E-GEOD-11303.idf.txt needs c3-4: done |
stress/zinc or Chemical effects/zinc |
03/04/13 |
+ |
+ |
+ |
complete (redone 5/9/13) |
|
Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol |
Affymetrix E. coli Genome 2.0 Array |
GSE35797 |
E-GEOD-35797 |
loaded 07/15/13 |
AMS c1-4 done |
JD E-GEOD-35797.idf.txt needs c3-4 |
Biofilms/drug treatment |
03/04/13 |
|||||
|
Identification of promoter sequence elements involved in specific recognition by the σS subunit of bacterial RNA polymerase. |
Affymetrix E. coli Genome 2.0 Array |
GSE22207 |
E-GEOD-22207 |
loaded 07/03/13 |
JD
E-GEOD-22207.idf.txt needs c3-4 |
promoter/sigma factor |
03/04/13 |
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|
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 |
Affymetrix E. coli Genome 2.0 Array |
GSE21604 |
E-GEOD-21604 |
loaded 06/24/13 |
JD
E-GEOD-21604.idf.txt needs c2-4 |
biofilm/mutagenesis |
03/04/13 |
||||||
|
The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain. |
Affymetrix E. coli Genome 2.0 Array |
GSE21893 |
E-GEOD-21893 |
loaded 07/11/13 |
JD
E-GEOD-21893.idf.txt needs c3-4 |
APEC/type VI secretion system |
03/05/13 |
||||||
|
BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type |
Affymetrix E. coli Genome 2.0 Array |
GSE34028 |
E-GEOD-34028 |
loaded 03/19/13 re-loaded 04/14/13 |
03/12/2013 - DAS |
JD
E-GEOD-34028.idf.txt needs c3-4: DAS added 3/12/2013 |
Persister cells/Mutant vs Wild-type |
03/05/13 |
+ |
+ |
+ |
complete (redone 5/7/13) | |
|
Persistence of BW25113 mqsR producing MqsR 2-1 vs. producing wild-type MqsR with ampicillin |
Affymetrix E. coli Genome 2.0 Array |
GSE31054 |
E-GEOD-31054 |
loaded 07/09/13 |
JD
E-GEOD-31054.idf.txt needs c3-4 |
Persister cells/Stress resistance |
03/05/13 |
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|
Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm |
Affymetrix E. coli Genome 2.0 Array |
GSE28193 |
E-GEOD-28193 |
loaded 6/28/13 |
JD
E-GEOD-28193.idf.txt needs c3-4 |
biofilm/honey |
03/05/13 |
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|
The E. coli deletion mutant of the nusB gene |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3335 |
loaded 5/15/13 |
4/4/13 - DAS |
JD needs c3-4 |
tRNA modificaton/transcript profiling |
03/05/13 |
+ |
+ |
+ |
complete 5/16/13 | ||
|
E. coli ygjD gene temperature sensitive mutant incubated at 37 oC |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3334 |
loaded 6/28/13 |
JD
E-MEXP-3334.idf.txt needs c1-4 |
tRNA modification/transcript profiling |
03/05/13 |
|||||||
|
The E. coli temperature-sensitive mutant of the ygjD gene incubated at 30°C. |
Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2] |
E-MEXP-3333 |
loaded 6/28/13 |
JD
E-MEXP-3333.idf.txt needs c2-4 |
tRNA modification/transcript profiling |
03/05/13 |
|||||||
|
Mechanisms of Biofilm Formation in Two Escherichia coli O157:H7 Lineages |
Affymetrix E. coli Genome 2.0 Array |
GSE19953 |
E-GEOD-19953 |
loaded 06/06/13 |
C1-C4 Complete AMS |
JD
E-GEOD-19953.idf.txt needs c3-4 |
EHEC/biofilm |
03/05/13 |
|||||
|
An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol. |
Affymetrix E. coli Genome 2.0 Array |
GSE18972 |
E-GEOD-18972 |
loaded 03/19/13 re-loaded 04/13/13 |
03/11/13 - DAS |
JD E-GEOD-18972.idf.txt needs c1-4 no cel files in ae |
biofuel/glycerol |
03/05/13 |
+ |
+ |
+ |
complete (redone 5/8/13) | |
|
QseA regulation of virulence factors in EHEC |
Affymetrix E. coli Genome 2.0 Array |
GSE18118 |
E-GEOD-18118 |
loaded 07/10/13 |
JD 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 |
Affymetrix E. coli Genome 2.0 Array |
GSE12701 |
E-GEOD-12701 |
was already loaded as part of publication: "Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae." together with E-GEOD-11932 |
c1-4 done, AMS 05/15/13 DAS sent idf, sdrf to JD |
JD
E-GEOD-12701.idf.txt needs c2-4 modified matrix file Absent->A, ... |
biofilm/toxin-antitoxin system |
03/05/13 |
+ |
+ |
+ |
complete | |
|
Effects of (E)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one (BF8) on E. coli RP437 persister cells (two biological replicates) |
unpublished |
Affymetrix E. coli Genome 2.0 Array |
GSE44273 |
E-GEOD-44273 |
loaded 6/25/13 |
JD E-GEOD-44273.idf.txt needs c1-4 |
persistence/transcript profiling |
03/06/13 |
|||||
|
Overexpression of BglJ and LeuO in Escherichia coli K12 |
Affymetrix E. coli Genome 2.0 Array |
GSE34023 |
loaded 07/08/13 |
JD: dataset not in ae, idf/sdrf made from scratch
E-GEOD-34023.idf.txt needs c1-4 |
Virulence/Regulation of gene expression |
03/06/13 |
|||||||
|
Expression data from laboratory evolution of Escherichia coli on lactate or glycerol |
Ecoli_ASv2 |
GSE33147 |
E-GEOD-33147 |
loaded 05/14/13 |
C1-4 done, AMS sent idf, sdrf to JD on 5/13/13 |
JD
E-GEOD-33147.idf.txt needs c3-4 |
evolution/carbon source |
03/07/13 |
+ |
+ |
+ |
complete | |
|
Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. |
Ecoli_ASv2 |
GSE5239 |
E-GEOD-5239 |
loaded 05/27/13 |
loaded 05/26/13 |
JD dataset has no cel files and only intensity values!
E-GEOD-5239.idf.txt |
plasmid/metabolism |
03/07/13 |
+ |
+ |
- (no cel files) |
complete (5/31/13) | |
|
Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains |
Ecoli_ASv2 |
GSE7398 (GSE7379 is the fis(del)subset, GSE7380 the wt) |
E-GEOD-7398 (E-GEOD-7379 is the fis(del)subset, E-GEOD-7380 the wt) |
loaded 06/07/13 |
C1-4 done, AMS |
JD
E-GEOD-7398.idf.txt needs c1-4 |
growth phase/fis |
03/07/13 |
|||||
|
Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media |
unpublished |
Ecoli_ASv2 |
E-TABM-103 |
in process |
JD: can't figure out how the experiment was done. |
03/07/13 |
|||||||
|
Global Transcriptional Programs Reveal a Carbon Source Foraging Strategy by Escherichia coli |
Ecoli_ASv2 |
GSE2037 |
E-GEOD-2037 |
loaded 6/28/13 |
JD E-GEOD-2037.idf.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. |
Ecoli_ASv2 |
GSE5818 |
E-GEOD-5818 |
loaded on 5/17/13 |
03/11/13 - DAS (waiting to hear from authors about strain background, but OK to load) |
JD: no cel files available E-GEOD-5818.idf.txt needs c1-4: DAS added on 3/11/13; DAS emailed Dick Burgess to ask if the strain background was MG1655 or MG1655K1 (a derivative of MG1655 that has the tetR gene inserted into the chromosome) flhDC o/e data are not in the dataset, this is probably because the paper reports no differences in transcript levels were observed before and after overexpression of flhD |
flagellum/regulation |
03/08/13 |
+ |
+ |
no - no cel files available |
complete 5/17/13 | |
|
Enterobactin is required for biofilm development in reduced-genome Escherichia coli |
Ecoli_ASv2 |
E-MEXP-1408 |
loaded 05/30/13 |
05/22/13 - DAS |
JD E-MEXP-1408.idf.txt needs c1-4 |
biofilm/transcription profiling DAS suggests biofilm/Reduced genome |
03/08/13 |
+ |
+ |
+ |
complete 05/30/13 | ||
|
Indole cell signaling occurs primarily at low temperatures in Escherichia coli |
Ecoli_ASv2 and E_coli_2 |
GSE9923 |
E-GEOD-9923 |
loaded 07/03/13 |
JD E-GEOD-9923.idf.txt needs c2-4 |
biofilm/indole |
03/08/13 |
||||||
|
Effect of RyhB Small RNA on Global Iron Use in Escherichia coli |
Ecoli_ASv2 |
GSE3105 |
E-GEOD-3105 |
loaded 5/16/13 |
04/16/13 - DAS DAS sent idf, sdrf to JD 05/14/13 |
JD: no cel files available |
iron/non-coding RNA |
03/08/13 |
+ |
+ |
no: no cel files |
complete 5/17/13 | |
|
sigma32 over-expression in E. coli |
Ecoli_ASv2 |
GSE2140 |
E-GEOD-2140 |
loaded 05/31/13 |
05/26/13 - DAS |
JD
E-GEOD-2140.idf.txt needs c2-4 no cel files available |
sigma factor/transcription profiling |
03/08/13 |
+ |
+ |
- (no cel files) |
complete (5/31/13) | |
|
Temporal gene-expression in Escherichia coli K-12 biofilms |
Ecoli_ASv2 |
GSE3905 |
E-GEOD-3905 |
loaded 07/11/13 |
JD no cel file available E-GEOD-3905.idf.txt needs c3-4 |
biofilm/transcription profiling |
03/08/13 |
||||||
|
Characterization and global gene expression of F− phenocopies during Escherichia coli biofilm formation |
Ecoli_ASv2 |
E-MEXP-1001 |
loaded 05/30/13 |
05/27/13 - DAS |
JD E-MEXP-1001.idf.txt needs c3-4 |
biofilm/F- phenocopy |
03/11/13 |
+ |
+ |
+ |
complete (06/05/13) | ||
|
Indole is an inter-species biofilm signal mediated by SdiA |
Ecoli_ASv2 |
GSE4562 |
E-GEOD-4562 |
loaded 07/03/13 |
JD E-GEOD-4562.idf.txt needs c3-4 |
biofilm/indole |
03/11/13 |
||||||
|
Quorum Sensing in Escherichia coli Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture |
Ecoli_ASv2 |
GSE9203 |
E-GEOD-9203 |
loaded 06/97/13 |
Created C1-C4 AMS |
JD: no cel files available
E-GEOD-9203.idf.txt needs c3-4 |
Quorum sensing/biofilm |
03/11/13 |
|||||
|
YliH (BssR) and YceP (BssS) Regulate Escherichia coli K-12 Biofilm Formation by Influencing Cell Signaling |
Ecoli_ASv2 |
GSE3937 |
E-GEOD-3937 |
loaded 5/26/13 |
05/21/13 - DAS |
JD: no cel files available
E-GEOD-3937.idf.txt needs c3-4
|
Quorum sensing/biofilm |
03/11/13 |
+ |
+ |
- (no cel files) |
complete (05/30/13) | |
|
Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA) |
Ecoli_ASv2 |
GSE8706 |
E-GEOD-8706 |
loaded |
C1-4 done, AMS 05/14/13: DAS sent idf/sdrf files to JD |
JD E-GEOD-8706.idf.txt needs c3-4 |
Quorum sensing/biofilm |
03/11/13 |
+ |
+ |
+ |
complete (6/05/13) | |
|
luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling |
Ecoli_ASv2 |
GSE9587 |
E-GEOD-9587 |
loaded 06/06/13) |
C1-C4 Complete AMS |
JD: one cel file is corrupted - GSM242209 - had to use chp files given E-GEOD-9587.idf.txt needs c3-4 paper talks about expts in low/high glucose, but only low glucose data are in the set. The other dataset is E-GEOD-9582 and it was loaded in 2010. |
Quorum sensing/(Mutant/wild-type) |
03/12/13 |
|||||
|
Escherichia coli Harboring a Natural IncF Conjugative F Plasmid Develops Complex Mature Biofilms by Stimulating Synthesis of Colanic Acid and Curli |
Ecoli_ASv2 |
E-MEXP-1145 |
loaded 5/15/13 |
04/03/13 - DAS |
JD: E-MEXP-953 is part of same pub - already in porteco
E-MEXP-1145.idf.txt |
Biofilm/F plasmid |
03/12/13 |
+ |
+ |
+ |
complete 5/15/13 | ||
|
YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport |
Ecoli_ASv2 |
loaded 07/15/13 |
AMS c1-4 done |
JD: no cel files available E-GEOD-3514.idf.txt needs c3-4 |
Quorum sensing/biofilm |
03/12/13 |
|||||||
|
YcfR (BhsA) Influences Escherichia coli Biofilm Formation through Stress Response and Surface Hydrophobicity |
Ecoli_ASv2 |
GSE5904 |
E-GEOD-5904 |
loaded 07/15/13 |
AMS c1-4 done |
JD:
no cel files available
E-GEOD-5904.idf.txt needs c3-4 |
Biofilm/transcription profiling |
03/12/13 |
|||||
|
Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803 |
Ecoli_ASv2 |
GSE5905 |
E-GEOD-5905 |
loaded 07/08/13 |
JD: no cel files available
E-GEOD-5905.idf.txt needs c3-4
|
biofuel/biotechnology |
03/12/13 |
||||||
|
A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS |
Affymetrix E. coli Genome 2.0 Array |
loaded 03/26/13 re-loaded 04/12/13 |
4/4/13 - DAS |
JD ready to load? - yes (4/4/13 DAS) |
Toxin-antitoxin system/transcription profiling |
03/22/13 |
+ |
+ |
+ |
complete (redone - 5/7/13) | |||
|
Evolutionary genome engineering using a restriction–modification system |
PMC3203608 |
Ecoli_ASv2 |
GSE21869 |
the experimental data are loaded: |
C1-4 done, AMS |
faked idf/sdrf |
Evolution/Parental strain Evolution/Evolved strain Evolution/Mutant |
Nov 2012 |
+ |
+ |
+ |
complete (redone 5/10/13) | |
|
Toxins Hha and CspD and Small RNA Regulator Hfq Are Involved in Persister Cell Formation Through MqsR in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
reload |
yes |
JD |
persister cells/toxin-antitoxin systems |
04/01/13 |
+ |
+ |
+ |
complete (5/14/13) | |||
|
The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli |
Affymetrix E. coli Genome 2.0 Array |
reload |
yes |
JD |
catabolite repression/non-coding RNA |
04/01/13 |
wasn't missing - did not need to reload | ||||||
|
A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP |
A-GEOD-1246.adf.txt A-GEOD-3051.adf.txt |
reload |
yes |
JD E-GEOD-3591.idf 2-channel |
aerobic anaerobic transition/(nitrite/nitrate) |
04/01/13 |
+ |
+ |
+ |
complete (redone 5/9/13) | |||
|
The PurR regulon in Escherichia coli K-12 MG1655 |
Affymetrix E. coli Genome 2.0 Array |
reload |
yes |
JD |
purine metabolism/transcript profiling OR Chemical effects/wild-type vs mutant |
04/01/13 |
+ |
+ |
+ |
complete (redone 5/8/13) | |||
|
Engineering a Novel c-di-GMP-Binding Protein for Biofilm Dispersal |
Affymetrix E. coli Genome 2.0 Array |
reload |
yes |
JD |
biofilm dispersal/transcript profiling |
04/01/13 |
+ |
+ |
+ |
complete (redone 5/8/13) | |||
|
Hfq Virulence Regulation in Enterohemorrhagic Escherichia coli O157:H7 Strain 86-24 [down-pointing small open triangle] |
Affymetrix E. coli Genome 2.0 Array |
reload |
yes |
JD |
type III secretion system/transcript profiling |
04/01/13 |
+ |
+ |
+ |
complete (redone 05/08/13) | |||
|
Apple Flavonoid Phloretin Inhibits Escherichia coli O157:H7 Biofilm Formation and Ameliorates Colon Inflammation in Rats [down-pointing small open triangle] |
Affymetrix E. coli Genome 2.0 Array |
reload |
yes |
JD |
biofilms/antioxidants |
04/01/13 |
+ |
+ |
+ |
complete (redone 5/7/13) | |||
|
Dynamic omics approach identifies nutrition-mediated microbial interactions. |
Affymetrix E. coli Genome 2.0 Array |
reload |
yes |
JD E-GEOD-18474.idf load only coli data |
co-culture/transcript profiling |
04/01/13 |
+ |
+ |
+ |
complete (redone 5/8/13) | |||
|
Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD |
Affymetrix E. coli Genome 2.0 Array Affymetrix E. coli Antisense Genome Array |
reload - expression data only |
yes |
JD E-GEOD-14203.idf two platforms - sdrf only contains data for genome 2.0 array |
toxin antitoxin systems/transcript profiling |
04/01/13 |
+ |
+ |
+ |
complete (redone 5/9/13) | |||
|
Molecular Strategy for Survival at a Critical High Temperature in Escherichia coli |
Affymetrix GeneChip E.coli Antisense Genome Array |
reload |
yes |
Heat shock/critical high temperature |
04/01/13 |
+ |
+ |
+ |
complete (redone 5/8/13) | ||||
|
Genome-wide transcriptional profiling on microarray was performed for strain MC4100 in comparison to its otherwise isogenic ycgE::cat derivative. Strains were grown in LB at 28°C and cells were harvested at an OD (578nm) of 4.0. |
A-MEXP-1444 |
E-MEXP-1872 |
reload |
yes |
blue-light response/two-component system |
+ |
+ |
+ |
complete (reloaded 5/14/13) | ||||
|
Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine |
Affymetrix GeneChip E.coli Genome 2.0 Array |
reload |
yes |
JD |
Asymptomatic Bacteriuria/transcription profiling |
04/01/13 |
+ |
= |
+ |
complete (redone 5/9/13) | |||
|
Transcription profiling of E. coli wild type and ycgF::kan cells treated with blue-light irradiation for 3 hours at 16oC |
A-MEXP-1444 |
E-MEXP-1877 |
reload |
yes |
blue-light response/two-component system |
+ |
+ |
+ |
complete (reloaded 5/14/13) | ||||
|
Time Course of Acid-Shifted, Aerobically Grown Escherichia coli K-12 W3110 |
PMID:18302792 |
Affymetrix E. coli Antisense Genome Array |
reloaded 6/25/13 |
redoing this data set because there was a problem with the original loading |
Stress/pH (external) |
06/21/2013 |
+ |
+ |
+ |
complete 06/25/13 | |||
|
changes of global gene expression in E. coli during an oxygen shift |
Affymetrix E. coli Antisense Genome Array |
GSE1121 GSE1106 GSE1107 |
E-GEOD-1121 |
reloaded 6/28/13 |
yes |
reloaded due to error during original loading |
(aerobic/anaerobic)/(mutant/wild-type) |
+ |
+ |
+ |
6/28/13 | ||
|
Transcription profiling of E. coli K-12 MG1655 and UTI89 harvested from gnotobiotic ceca 14 days post-inoculation |
PMID:17504765 |
Affymetrix E. coli Antisense Genome Array |
reloaded 7/02/13 |
yes |
redoing this data set because there was a problem with the original loading |
Strain comparison/(Anaerobic growth/Aerobic Growth) |
+ |
+ |
+ |
complete 07/02/13 | |||
|
Transcription profiling of E. coli K-12 MG1655 and UTI89 in vitro culture - time series |
PMID:17504765 |
Affymetrix E. coli Antisense Genome Array |
reloaded 7/02/13 |
yes |
redoing this data set because there was a problem with the original loading |
Strain comparison/cecum |
+ |
+ |
+ |
complete 07/02/13 | |||
|
GSE26591 |
E-GEOD-26591 |
loaded (partially, as E-GEOD-26588) |
JD: this is a superset of expression data (E-GEOD-26588) and chip-chip data. The expression data is loaded |
||||||||||
|
Transcription profiling by array of Escherichia coli (strain MG1655) to study cellular responses to the oxidizing effects of bleach |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-3639 |
loaded 07/16/13 |
needs c1 - c4 |
bleach/transcription profiling |
07/16/13 |
|||||||
|
Transcription profiling by array of wild-type E. coli W3110 and hns, stpA, hha, ydgT mutants |
Affymetrix GeneChip E.coli Genome 2.0 Array |
E-MEXP-3811 |
loaded 07/16/13 |
JD needs c1-4 |
nucleoid/transcript profiling |
07/16/13 |
|||||||
|
Transcription profiling of E.coli reveals indole cell signaling occurs primarily at low temperatures in Escherichia coli |
Affymetrix GeneChip E.coli Antisense Genome Array |
GSE9923 |
E-GEOD-9923 |
loaded (partially) |
JD: 4 slides from antisense platform are not loaded |
||||||||
|
Enterohemorrhagic Escherichia coli (EHEC) 86-24 double deletions of kdpE and cra grown in DMEM |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE43659 |
E-GEOD-43659 |
loaded 07/16/13 |
07/23/13 - DAS updated idf,sdrf |
JD: needs c1-c4 |
virulence/transcript profiling |
07/16/13 |
+ |
+ |
+ |
07/23/13 | |
|
Expression data from Avian Pathogenic Escherichia coli |
not published |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE48015 |
E-GEOD-48015 |
loaded 07/17/13 |
APEC/transcript profiling |
07/17/13 |
||||||
|
Expression data of Enterohemorrhagic E. coli O157:H7 (EHEC) strain 86-24 when cultured with Bacteroides thetaiotaomicron VPI-5482 |
not published |
Affymetrix GeneChip E.coli Genome 2.0 Array |
GSE47418 |
E-GEOD-47418 |
loaded 07/17/13 |
EHEC/co-culture |
07/17/13 |
||||||
|
Expression profiling of wt and ydcR mutant strains |
not published |
E. coli Genome 2.0 Array |
GSE48776 |
not yet in AE |
in process |
JD: wait for mage_tab files |
| ||||||
| edit table |
</protect>
- ↑ Messaoudi, N et al. (2013) Global stress response in a prokaryotic model of DJ-1-associated Parkinsonism. J. Bacteriol. 195 1167-78 PubMed
- ↑ Pacheco, AR et al. (2012) Fucose sensing regulates bacterial intestinal colonization. Nature 492 113-7 PubMed
- ↑ Kamenšek, S & Žgur-Bertok, D (2013) Global transcriptional responses to the bacteriocin colicin M in Escherichia coli. BMC Microbiol. 13 42 PubMed
- ↑ Fried, L et al. (2013) Identification of a target gene and activating stimulus for the YpdA/YpdB histidine kinase/response regulator system in Escherichia coli. J. Bacteriol. 195 807-15 PubMed
- ↑ Yang, C et al. (2012) Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli. PLoS ONE 7 e47314 PubMed
- ↑ Bansal, T et al. (2012) Human intestinal epithelial cell-derived molecule(s) increase enterohemorrhagic Escherichia coli virulence. FEMS Immunol. Med. Microbiol. 66 399-410 PubMed
- ↑ Visvalingam, J et al. (2013) Examination of the genome-wide transcriptional response of Escherichia coli O157:H7 to cinnamaldehyde exposure. Appl. Environ. Microbiol. 79 942-50 PubMed
- ↑ Arunasri, K et al. (2013) Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression. PLoS ONE 8 e57860 PubMed
- ↑ Santos, CN et al. (2012) Rational, combinatorial, and genomic approaches for engineering L-tyrosine production in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 109 13538-43 PubMed
- ↑ Chattopadhyay, MK et al. (2013) Escherichia coli glutathionylspermidine synthetase/amidase: phylogeny and effect on regulation of gene expression. FEMS Microbiol. Lett. 338 132-40 PubMed
- ↑ Hu, Y et al. (2012) Antitoxin DinJ influences the general stress response through transcript stabilizer CspE. Environ. Microbiol. 14 669-79 PubMed
- ↑ Lee, JH et al. (2012) Indole-3-acetaldehyde from Rhodococcus sp. BFI 332 inhibits Escherichia coli O157:H7 biofilm formation. Appl. Microbiol. Biotechnol. 96 1071-8 PubMed
- ↑ Kendall, MM et al. (2012) Ethanolamine controls expression of genes encoding components involved in interkingdom signaling and virulence in enterohemorrhagic Escherichia coli O157:H7. MBio 3 PubMed
- ↑ Ma, Q & Wood, TK (2011) Protein acetylation in prokaryotes increases stress resistance. Biochem. Biophys. Res. Commun. 410 846-51 PubMed
- ↑ Huwiler, SG et al. (2012) Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields. Bioelectromagnetics 33 488-96 PubMed
- ↑ Le Gac, M et al. (2012) Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 109 9487-92 PubMed
- ↑ Hancock, V et al. (2010) Functional genomics of probiotic Escherichia coli Nissle 1917 and 83972, and UPEC strain CFT073: comparison of transcriptomes, growth and biofilm formation. Mol. Genet. Genomics 284 437-54 PubMed
- ↑ Potrykus, K et al. (2010) Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. Nucleic Acids Res. 38 1636-51 PubMed
- ↑ Critzer, FJ et al. (2010) Increased transcription of the phosphate-specific transport system of Escherichia coli O157:H7 after exposure to sodium benzoate. J. Food Prot. 73 819-24 PubMed
- ↑ Mensa, B et al. (2011) Antibacterial mechanism of action of arylamide foldamers. Antimicrob. Agents Chemother. 55 5043-53 PubMed
- ↑ Kocharunchitt, C et al. (2012) Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress. Mol. Cell Proteomics 11 M111.009019 PubMed
- ↑ Hancock, V & Klemm, P (2007) Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine. Infect. Immun. 75 966-76 PubMed
- ↑ Watts, RE et al. (2010) Escherichia coli isolates causing asymptomatic bacteriuria in catheterized and noncatheterized individuals possess similar virulence properties. J. Clin. Microbiol. 48 2449-58 PubMed
- ↑ Johnson, BJ et al. (2008) Impact of cranberry on Escherichia coli cellular surface characteristics. Biochem. Biophys. Res. Commun. 377 992-4 PubMed
- ↑ Isalan, M et al. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452 840-5 PubMed
- ↑ 26.0 26.1 26.2 Sharma, AK et al. (2011) Comparative transcriptomic profile analysis of fed-batch cultures expressing different recombinant proteins in Escherichia coli. AMB Express 1 33 PubMed
- ↑ Singh, AB et al. (2012) Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon-beta in high cell density fed batch cultures using time course transcriptomic data. Mol Biosyst 8 615-28 PubMed
- ↑ Withman, B et al. (2013) Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea. Infect. Immun. 81 80-9 PubMed
- ↑ Holm, AK et al. (2010) Metabolic and transcriptional response to cofactor perturbations in Escherichia coli. J. Biol. Chem. 285 17498-506 PubMed
- ↑ Glover, WA et al. (2009) Insights into the molecular basis of L-form formation and survival in Escherichia coli. PLoS ONE 4 e7316 PubMed
- ↑ Seth, D et al. (2012) Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR. Science 336 470-3 PubMed
- ↑ Njoroge, J & Sperandio, V (2012) Enterohemorrhagic Escherichia coli virulence regulation by two bacterial adrenergic kinases, QseC and QseE. Infect. Immun. 80 688-703 PubMed
- ↑ 33.0 33.1 Chu, W et al. (2012) Indole production promotes Escherichia coli mixed-culture growth with Pseudomonas aeruginosa by inhibiting quorum signaling. Appl. Environ. Microbiol. 78 411-9 PubMed
- ↑ Strader, MB et al. (2011) A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. Mol. Cell Proteomics 10 M110.005199 PubMed
- ↑ 35.0 35.1 Nam, H et al. (2012) Network context and selection in the evolution to enzyme specificity. Science 337 1101-4 PubMed
- ↑ Chen, T et al. (2012) Significant rewiring of the transcriptome and proteome of an Escherichia coli strain harboring a tailored exogenous global regulator IrrE. PLoS ONE 7 e37126 PubMed
- ↑ Kraxenberger, T et al. (2012) First insights into the unexplored two-component system YehU/YehT in Escherichia coli. J. Bacteriol. 194 4272-84 PubMed
- ↑ Wang, J et al. (2012) Global regulator engineering significantly improved Escherichia coli tolerances toward inhibitors of lignocellulosic hydrolysates. Biotechnol. Bioeng. 109 3133-42 PubMed
- ↑ Lu, W et al. (2013) Genome-wide transcriptional responses of Escherichia coli to glyphosate, a potent inhibitor of the shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase. Mol Biosyst 9 522-30 PubMed
- ↑ Li, L et al. (2009) A novel RPMXR motif among class II 5-enolpyruvylshikimate-3-phosphate synthases is required for enzymatic activity and glyphosate resistance. J. Biotechnol. 144 330-6 PubMed
- ↑ Gupta, P et al. () A single nucleotide polymorphism in ycdC alters tRNA synthetase expression and results in hypersecretion in Escherichia coli. Biotechnol. Prog. 28 646-53 PubMed
- ↑ Warner, DM & Levy, SB (2012) SoxS increases the expression of the zinc uptake system ZnuACB in an Escherichia coli murine pyelonephritis model. J. Bacteriol. 194 1177-85 PubMed
- ↑ Hensley, MP et al. (2012) Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli. J. Inorg. Biochem. 111 164-72 PubMed
- ↑ Lim, JY et al. (2012) Dimethyl sulfoxide and ethanol elicit increased amyloid biogenesis and amyloid-integrated biofilm formation in Escherichia coli. Appl. Environ. Microbiol. 78 3369-78 PubMed
- ↑ Maciag, A et al. (2011) In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements. Nucleic Acids Res. 39 5338-55 PubMed
- ↑ Hong, SH et al. (2010) Engineering global regulator Hha of Escherichia coli to control biofilm dispersal. Microb Biotechnol 3 717-28 PubMed
- ↑ de Pace, F et al. (2010) The type VI secretion system plays a role in type 1 fimbria expression and pathogenesis of an avian pathogenic Escherichia coli strain. Infect. Immun. 78 4990-8 PubMed
- ↑ 48.0 48.1 Hong, SH et al. (2012) Bacterial persistence increases as environmental fitness decreases. Microb Biotechnol 5 509-22 PubMed
- ↑ Lee, JH et al. (2011) Low concentrations of honey reduce biofilm formation, quorum sensing, and virulence in Escherichia coli O157:H7. Biofouling 27 1095-104 PubMed
- ↑ 50.0 50.1 50.2 Hashimoto, C et al. (2011) Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli. J. Bacteriol. 193 6075-9 PubMed
- ↑ Lee, JH et al. (2011) Transcriptomic analysis for genetic mechanisms of the factors related to biofilm formation in Escherichia coli O157:H7. Curr. Microbiol. 62 1321-30 PubMed
- ↑ Hu, H & Wood, TK (2010) An evolved Escherichia coli strain for producing hydrogen and ethanol from glycerol. Biochem. Biophys. Res. Commun. 391 1033-8 PubMed
- ↑ Kendall, MM et al. (2010) The LysR-type regulator QseA regulates both characterized and putative virulence genes in enterohaemorrhagic Escherichia coli O157:H7. Mol. Microbiol. 76 1306-21 PubMed
- ↑ Kim, Y et al. (2009) Toxin-antitoxin systems in Escherichia coli influence biofilm formation through YjgK (TabA) and fimbriae. J. Bacteriol. 191 1258-67 PubMed
- ↑ Stratmann, T et al. (2012) RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants. Mol. Microbiol. 83 1109-23 PubMed
- ↑ Fong, SS et al. (2005) Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res. 15 1365-72 PubMed
- ↑ Wang, Z et al. (2006) Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb. Cell Fact. 5 34 PubMed
- ↑ Bradley, MD et al. (2007) Effects of Fis on Escherichia coli gene expression during different growth stages. Microbiology (Reading, Engl.) 153 2922-40 PubMed
- ↑ Liu, M et al. (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J. Biol. Chem. 280 15921-7 PubMed
- ↑ Zhao, K et al. (2007) Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli. Nucleic Acids Res. 35 4441-52 PubMed
- ↑ May, T & Okabe, S (2011) Enterobactin is required for biofilm development in reduced-genome Escherichia coli. Environ. Microbiol. 13 3149-62 PubMed
- ↑ Lee, J et al. (2008) Indole cell signaling occurs primarily at low temperatures in Escherichia coli. ISME J 2 1007-23 PubMed
- ↑ Massé, E et al. (2005) Effect of RyhB small RNA on global iron use in Escherichia coli. J. Bacteriol. 187 6962-71 PubMed
- ↑ Zhao, K et al. (2005) The global transcriptional response of Escherichia coli to induced sigma 32 protein involves sigma 32 regulon activation followed by inactivation and degradation of sigma 32 in vivo. J. Biol. Chem. 280 17758-68 PubMed
- ↑ Domka, J et al. (2007) Temporal gene-expression in Escherichia coli K-12 biofilms. Environ. Microbiol. 9 332-46 PubMed
- ↑ May, T et al. (2010) Characterization and global gene expression of F- phenocopies during Escherichia coli biofilm formation. Mol. Genet. Genomics 284 333-42 PubMed
- ↑ Lee, J et al. (2007) Indole is an inter-species biofilm signal mediated by SdiA. BMC Microbiol. 7 42 PubMed
- ↑ Li, J et al. (2007) Quorum sensing in Escherichia coli is signaled by AI-2/LsrR: effects on small RNA and biofilm architecture. J. Bacteriol. 189 6011-20 PubMed
- ↑ Domka, J et al. (2006) YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling. Appl. Environ. Microbiol. 72 2449-59 PubMed
- ↑ Zhang, XS et al. (2008) Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA). ISME J 2 615-31 PubMed
- ↑ Wang, L et al. (2005) luxS-dependent gene regulation in Escherichia coli K-12 revealed by genomic expression profiling. J. Bacteriol. 187 8350-60 PubMed
- ↑ May, T & Okabe, S (2008) Escherichia coli harboring a natural IncF conjugative F plasmid develops complex mature biofilms by stimulating synthesis of colanic acid and Curli. J. Bacteriol. 190 7479-90 PubMed
- ↑ Herzberg, M et al. (2006) YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. J. Bacteriol. 188 587-98 PubMed
- ↑ Zhang, XS et al. (2007) YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity. J. Bacteriol. 189 3051-62 PubMed
- ↑ Maeda, T et al. (2007) Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803. BMC Biotechnol. 7 25 PubMed
- ↑ Wang, X et al. (2012) A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat. Chem. Biol. 8 855-61 PubMed
- ↑ Asakura, Y et al. (2011) Evolutionary genome engineering using a restriction-modification system. Nucleic Acids Res. 39 9034-46 PubMed
- ↑ Kim, Y & Wood, TK (2010) Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem. Biophys. Res. Commun. 391 209-13 PubMed
- ↑ Beisel, CL & Storz, G (2011) The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli. Mol. Cell 41 286-97 PubMed
- ↑ Constantinidou, C et al. (2006) A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J. Biol. Chem. 281 4802-15 PubMed
- ↑ Hobman, JL et al. (2007) Comparative genomic hybridization detects secondary chromosomal deletions in Escherichia coli K-12 MG1655 mutants and highlights instability in the flhDC region. J. Bacteriol. 189 8786-92 PubMed
- ↑ Cho, BK et al. (2011) The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res. 39 6456-64 PubMed
- ↑ Ma, Q et al. (2011) Engineering a novel c-di-GMP-binding protein for biofilm dispersal. Environ. Microbiol. 13 631-42 PubMed
- ↑ Kendall, MM et al. (2011) Hfq virulence regulation in enterohemorrhagic Escherichia coli O157:H7 strain 86-24. J. Bacteriol. 193 6843-51 PubMed
- ↑ Lee, JH et al. (2011) Apple flavonoid phloretin inhibits Escherichia coli O157:H7 biofilm formation and ameliorates colon inflammation in rats. Infect. Immun. 79 4819-27 PubMed
- ↑ Nakanishi, Y et al. (2011) Dynamic omics approach identifies nutrition-mediated microbial interactions. J. Proteome Res. 10 824-36 PubMed
- ↑ Kim, Y et al. (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ. Microbiol. 12 1105-21 PubMed
- ↑ Murata, M et al. (2011) Molecular strategy for survival at a critical high temperature in Eschierichia coli. PLoS ONE 6 e20063 PubMed
- ↑ 89.0 89.1 Tschowri, N et al. (2009) The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev. 23 522-34 PubMed
- ↑ Vejborg, RM et al. (2012) Identification of genes important for growth of asymptomatic bacteriuria Escherichia coli in urine. Infect. Immun. 80 3179-88 PubMed
- ↑ Gray, MJ et al. (2013) NemR is a bleach-sensing transcription factor. J. Biol. Chem. 288 13789-98 PubMed
- ↑ Njoroge, JW et al. (2013) The interacting Cra and KdpE regulators are involved in the expression of multiple virulence factors in enterohemorrhagic Escherichia coli. J. Bacteriol. 195 2499-508 PubMed
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