Category:Expression data
The PortEco team is collecting E. coli microarray data into one database. Click here to link to the PortEco Expression database.
The list below provides links to the literature pages in EcoliWiki for papers that contain microarray data. (Note: this list is still in progress.)
<protect>
| Type | Reference | Description | Platform | GEO | ArrayExpress | SMD | GenExpDB | Notes |
|---|---|---|---|---|---|---|---|---|
|
microarray |
Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933 |
Affymetrix E_coli_2 |
- |
|||||
|
microarray |
E. coli K-12 str. P4X grown with the arginine regulon fully repressed, partially repressed, or fully derepressed (argR). |
Affymetrix E_coli_2 |
loaded 2/8/10 Publication: Caldera 2006 |
Added strain page for P4X to EcoliWiki. | ||||
|
microarray |
E. coli K-12 str. W3110 oxygen downshift |
Affymetrix E_coli_2 |
loaded 2/7/10 Publication: Soini 2008 |
- |
||||
|
microarray |
E. coli K-12 strain Frag1 in response to ionic and non-ionic osmotica |
Affymetrix E_coli_2 |
loaded 2/12/2010 Publication:Shabala 2009 |
- |
||||
|
microarray |
E. coli K-12 BW25113/pCA24N-hha with 2 mM IPTG vs BW25113/pCA24N with 2 mM IPTG |
Affymetrix E_coli_2 |
loaded 2/7/2010 |
|||||
|
microarray |
E. coli K-12 MG1655 and E. coli O157:H7 EDL933 inhibited for Rho activity to assess Rho function |
Affymetrix E_coli_2 |
loaded 2/7/2010 |
Made a strain page for minimal genome strain MDS42 in EcoliWiki. The text says that a nusG(del) mutation was used, but the strain table in the supplemental material gives the genotype of RSW422 as MDS42 nusG::Kan. Is this a typo? | ||||
|
microarray |
E.coli K-12 MG1655 and BW25113 ∆soxR::kan treated with paraquat - time series |
Affymetrix E_coli_2 |
loaded 2/8/2010 Publication: Blanchard 2007 |
BW25113 is a derivative of MG1655 and is the parent strain for the Keio collection of deletion mutants. | ||||
|
microarray |
E.coli K-12 W3110 and the isogenic phoU::miniTn10Kan mutant |
Affymetrix E_coli_2 |
loaded 2/8/2010 Publication:Li 2007 |
|||||
|
microarray |
E. coli O157:H7 str. EDL933 biofilms treated with 7-hydroxyindole and isatin |
Affymetrix E_coli_2 |
loaded 2/7/2010 |
|||||
|
microarray |
E. coli O157:H7 strain EDL933 LB-Glu 7 hr biofilm cells with various chemicals |
Affymetrix E_coli_2 |
loaded 2/8/2010 Publication: Bansal 2007 |
|||||
|
microarray |
Alper H and Stephanopoulos G (2007) Metab Eng 9(3):258-67 |
E. coli K-12 DH5alpha with plasmid-borne wild-type and mutant rpoD alleles grown in the presence and absence of ethanol |
Affymetrix E_coli_2 |
loaded 2/8/2010 Publication:Alper 2007 |
||||
|
microarray |
E.coli EHEC lux::tet strain (VS94) grown in SAPI medium in the presence of AI-2, time series experiment |
Affymetrix E_coli_2 |
loaded 2/12/2010 Publication:Bansal 2008 |
- |
||||
|
microarray |
E. coli asymptomatic bacteriuria (ABU) strain 83972 grown on urine-agar plates or cultured in MOPS-glucose medium |
Affymetrix E_coli_2 |
- |
|||||
|
microarray |
E. coli asymptomatic bacteriuria (ABU) strains 83972 and VR50 during biofilm growth in human urine compared to planktonic cells |
Affymetrix E_coli_2 |
- |
|||||
|
microarray |
E. coli K-12 TOP10 cells containing rewired gene network constructs |
Affymetrix E_coli_2 |
- |
|||||
|
microarray |
E. coli asymptomatic bacteriuria (ABU) strain 83972 grown in MOPS minimal glucose medium, in urine, and in 3 individual patients |
Affymetrix E_coli_2 |
- |
|||||
|
microarray |
E. coli MG1655 treated with CHIR-090, an inhibitor of lipid A biosythesis |
Affymetrix E_coli_2 |
- |
CHIR-090 (10X MIC) or DMSO (solvent) | ||||
|
microarray |
E.coli K-12 strains BW25113 and BW25113 ∆CP4-57, where the CP4-57 prophage has been excised, cultured in LB medium at 37°C |
Affymetrix E_coli_2 |
- |
|||||
|
microarray |
E. coli K-12 MG1655 pOX38Km comparison of cells isolated from the outside and inside of biofilms and exponential and stationary phase planktonic cultures. |
Affymetrix E_coli_2 |
loaded 2/7/2010 Publication:Ito 2009 |
- |
Added pOX38Km to EcoliWiki. Paper uses pOX38Km rpoS-gfp.) | |||
|
microarray |
E. coli K-12 MG1655 and isogenic strain LVM100, which has 5 toxin-antitoxin (TA) gene pairs deleted, examined during biofilm development |
Affymetrix E_coli_2 |
|
- |
||||
|
microarray |
E. coli K-12 BW25113 and BW25113 yjgK(del)::kan strain grown for 8 h in LB, glass wool biofilms |
Affymetrix E_coli_2 |
loaded 2/12/2010 |
- |
Check whether the mutant used is one of the Keio deletions. | |||
|
microarray |
E. coli K-12 ATCC 25404 biofilms treated with 10 uM 5-fluorouracil vs. E. coli K-12 ATCC 25404 DMF-treated control biofilm |
Affymetrix E_coli_2 |
loaded 2/12/2010 Publication:Attila 2009 |
- |
||||
|
microarray |
E. coli K-12 MG1655 growing aerobically and anaerobically treated with the CO-releasing molecule CORM-2 (tricarbonyldichlororuthenium(II) dimer) |
Affymetrix E_coli_2 |
- |
|||||
|
microarray |
E. coli BW25113 K-12 hfq vs. wild-type persister |
Affymetrix E_coli_2 |
DAS |
- |
||||
|
microarray |
Effects of overexpression of the sRNA MgrR in E. coli K-12 str. KM100 mgrR(del)::FRT-kan-FRT and comparison of E. coli K-12 str. MG1655 araBAD(del) leu+ and MG1655 araBAD(del) leu+ mgrR(del)::FRT-kan-FRT |
Affymetrix E_coli_2 |
loaded 2/6/10 |
- |
||||
|
microarray |
E. coli O157:H7 86-24 parent and signaling mutants to investigate bacterial adrenergic signaling (norepinephrine, xx, xx) |
Affymetrix E_coli_2 |
- |
Check whether kan marker was flipped out. Used Dulbecco's modified Eagle's medium | ||||
|
microarray |
E. coli K-12 BW25113 vs. BW25113 ∆yncC742::FRT-kan-FRT grown in biofilms on glass wool and MG1655 vs MG1655 ∆yncC742::FRT-kan-FRT colony biofilms. All biofilms grown in LB medium for 15h at 37°C |
Affymetrix Ecoli_2 and Ecoli_ASv2 |
|
|||||
|
microarray |
E. coli metabolically engineered strains exposed to cis-1,2-dichloroethylene (cis-DCE) |
Affymetrix Ecoli_ASv2 |
- |
error: 2 different types of platforms E_coli_2.cdf and E_coli_ASv2.cdf GSE13698 E. coli cis-DCE mineralization and new stress genes <c-anno><c-1>E. coli K12 TG1 TOM-Green/IsoILR1/GSHI* and vector alone</c-1><c-2></c-2><c-3> LB at 37C</c-3><c-4>cis-1,2-dichloroethylene (cis-DCE)</c-4></c-anno> | ||||
|
microarray |
E. coli treated with cefsulodin and mecillinam |
Affymetrix E_coli_2 |
E-GEOD-10159 |
loaded 2/6/2010 |
One of the superseries contained in GSE10160. Are there two publications for Laubacher and Ades at the omics site? | |||
|
microarray |
E.coli indole cell signaling occurs primarily at low temperatures |
Affymetrix Ecoli_ASv2 |
||||||
|
microarray |
DpiA overexpression |
ecoli_12 |
||||||
|
microarray |
Tryptophan metabolism response in E. coli |
ecoli_3.0 |
||||||
|
microarray |
Tryptophan metabolism response in E. coli |
ecoli_4.3 |
||||||
|
microarray |
DpiA overexpression |
ECD3 |
||||||
|
microarray |
Global analysis of mRNA decay and abundance in Escherichia coli |
ECD1a-list1 |
||||||
|
microarray |
RNase G complementation of rne null mutation identifies functional interrelationships with RNase E |
ecoli_9.0 |
||||||
|
microarray |
Global analysis of Escherichia coli RNA degradosome function |
ECD1a-list1 |
||||||
|
microarray |
UV Exposure in Wild-Type and SOS-Deficient E. coli |
ecoli_4.3 |
||||||
|
microarray |
UV Exposure in Wild-Type and SOS-Deficient E. coli |
ecoli_8.0 |
||||||
|
microarray |
RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli |
ECD1a-list1 |
y |
|||||
|
microarray |
Adaptation to famine |
ecoli_12 |
||||||
|
microarray |
Gene expression in MG1655 and knock-out mutants during aerobic growth |
Affymetrix Ecoli_ASv2 |
E-GEOD-1121 |
Loaded 2/22/10 |
GSE1106 is a subset of GSE1121 (changes of global gene expression in E. coli during an oxygen shift) At what temp were cultures grown? Knock-out mutations were made by lambda red recombination. Do they still have a drug resistance marker? | |||
|
microarray |
gene expression in knock-out mutants during anaerobic growth |
Affymetrix Ecoli_ASv2 |
Loaded 2/24/10 |
SubSeries GSE1107 is part of SuperSeries: GSE1121 changes of global gene expression in E. coli during an oxygen shift | ||||
|
microarray |
changes of global gene expression in E. coli during an oxygen shift |
Affymetrix Ecoli_ASv2 |
E-GEOD-1121 |
GSE1106 and GSE1107 were loaded separately, and have been combined in a single publication. Was this correct? need to check references Publication Covert et al. (2004) |
y |
GSE1121 combines subseries GSE1106 and GSE1107. | ||
|
microarray |
carbon utilization in E. coli |
Affymetrix Ecoli_ASv2 |
E-GEOD-2037 |
y |
Missing Supplementary Files On GEO | |||
|
microarray |
sigma32 over-expression in E. coli |
Affymetrix Ecoli_ASv2 |
GSE2140 |
E-GEOD-2140 |
y |
Missing Supplementary Files On GEO | ||
|
microarray |
Effect of small RNA RyhB on global iron use in Escherichia coli |
Affymetrix Ecoli_ASv2 |
GSE3105 |
E-GEOD-3105 |
y |
Missing Supplementary Files On GEO | ||
|
microarray |
Differential gene expression of ydgG mutant |
Affymetrix Ecoli_ASv2 |
GSE3514 |
E-GEOD-3514 |
y |
Missing Supplementary Files On GEO | ||
|
microarray |
Temporal Biofilm Expression of E. coli K-12 after 4, 7, 15, and 24 hr |
Affymetrix Ecoli_ASv2 |
GSE3905 |
E-GEOD-3905 |
y |
Missing Supplementary Files On GEO | ||
|
microarray |
E. coli K-12 yliH and yceP biofilm expression relative to wild type |
Affymetrix Ecoli_ASv2 |
GSE3937 |
E-GEOD-3937 |
y |
Missing Supplementary Files On GEO | ||
|
microarray |
pH Regulates Genes for Flagellar Motility, Catabolism, and Oxidative Stress in Escherichia coli K-12 |
Affymetrix Ecoli_ASv2 |
E-GEOD-4511 |
y |
||||
|
microarray |
pH and Anaerobiosis Coregulate Metabolism, Multidrug Transporters, and Envelope Composition in Escherichia coli K-12 |
Affymetrix Ecoli_ASv2 |
E-GEOD-4556 |
y |
||||
|
microarray |
E. coli K-12 mutants yceP, trpE, and tnaA biofilm cell 24 hr for indole paper |
Affymetrix Ecoli_ASv2 |
E-GEOD-4562 |
y |
||||
|
microarray |
E. coli K-12 W3110 time course after acid-shift of aerobically grown cultures |
Affymetrix Ecoli_ASv2 |
E-GEOD-4778 |
loaded 3/07/10 |
y |
|||
|
microarray |
Expression data from Escherichia coli |
Affymetrix Ecoli_ASv2 |
GSE5239 |
E-GEOD-5239 |
y |
Missing Supplementary Files On GEO | ||
|
microarray |
- |
flagellar regulon studies |
Affymetrix Ecoli_ASv2 |
GSE5818 |
E-GEOD-5818 |
Missing Supplementary Files On GEO | ||
|
microarray |
E. coli K-12 mutant ycfR biofilm vs wild type 15 hr LB glu biofilm cells |
Affymetrix Ecoli_ASv2 |
E-GEOD-5904 |
y |
Missing Supplementary Files On GEO | |||
|
microarray |
E. coli TG1/pBS(Kan)Synhox and pBS(Kan) hydrogen production |
Affymetrix Ecoli_ASv2 |
E-GEOD-5905 |
y |
Missing Supplementary Files On GEO | |||
|
microarray |
Expression data from time courses of E. coli MG1655 and UTI89 in vitro |
Affymetrix Ecoli_ASv2 |
E-GEOD-6425 |
loaded 6/24/10 |
y |
|||
|
microarray |
E. coli K-12 MG1655 expression data from gnotobiotic ceca 14d post-inoculation |
Affymetrix Ecoli_ASv2 |
E-GEOD-6426 |
|
y |
|||
|
microarray |
Large-Scale Mapping and Validation of E. coli Transcriptional Regulation from a Compendium of Expression Profiles. |
Affymetrix Ecoli_ASv2 |
E-GEOD-6836 |
y |
||||
|
microarray |
E. coli K-12 wild type with R1drd19 biofilm vs wild type without R1drd19 biofilm |
Affymetrix Ecoli_ASv2 |
E-GEOD-6923 |
loaded 6/26/10 |
y |
|||
|
microarray |
BW25113 ymgB and W/T in LBglu 24h biofilm cells |
Affymetrix Ecoli_ASv2 |
E-GEOD-6925 |
loaded June 15, 2010 |
||||
|
microarray |
Expression profiles during cell death programmed by a restriction-modification system in E. coli |
Affymetrix Ecoli_ASv2 |
E-GEOD-7326 |
Loaded 5/18/2010 |
||||
|
microarray |
Fis KO strain |
Affymetrix Ecoli_ASv2 |
E-GEOD-7379 |
Partially Completed (see notes) |
There is an error. Please see Microarray_errors | |||
|
microarray |
WT (Fis+) strain |
Affymetrix Ecoli_ASv2 |
E-GEOD-7380 |
error (see notes) |
wrong CEL chiptype expecting "Ecoli_ASv2" instead of "Ecoli_antisense". Need a different .CDF | |||
|
microarray |
Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains |
Affymetrix Ecoli_ASv2 |
E-GEOD-7398 |
Related to GSE7380 (see microarry above) which has errors |
y |
|||
|
microarray |
Gene expression of E. coli MG1655 wild type and rpoS knock-out strains |
Affymetrix Ecoli_ASv2 |
E-GEOD-7885 |
|
||||
|
microarray |
BW25113 hha mutant vs wild type biofilm cells 4hr LB and 4,15,24hr LB glu |
Affymetrix Ecoli_ASv2 |
E-GEOD-8708 |
|
y |
|||
|
microarray |
- |
Expression profile for early stationary phase E. coli W3110 expression profile |
Affymetrix Ecoli_ASv2 |
E-GEOD-9203 |
Missing Supplementary Files On GEO | |||
|
microarray |
luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling |
Affymetrix Ecoli_ASv2 |
E-GEOD-9582 |
|
y |
|||
|
microarray |
luxS-Dependent Gene Regulation in Escherichia coli K-12 Revealed by Genomic Expression Profiling (II) |
Affymetrix Ecoli_ASv2 |
E-GEOD-9587 |
in progress...error (see notes) batch was created anyway (June 3, 2010) |
y |
FATAL ERROR: Failure in MAS5 execution | ||
|
microarray |
Tannin resistance strategies of Escherichia coli in anaerobic conditions |
Affymetrix Ecoli_ASv2 |
E-GEOD-9755 |
y |
||||
|
microarray |
RpoS regulation of gene expression during exponential growth of E. coli K-12 |
Affymetrix Ecoli_ASv2 |
E-GEOD-9814 |
|
y |
rpoS(del)::FRT (pers. comm. H. Schellhorn 6/15/10) | ||
|
microarray |
Expression of Escherichia coli treated with cefsulodin and mecillinam, alone and in combination |
Affymetrix Ecoli_ASv2 |
E-GEOD-10158 |
6/11/10 |
One of the subseries contained in GSE10160. Are there two publications for Laubacher and Ades at the omics site? | |||
|
microarray |
Expression profiles of E. coli groESL(-) cells expressing human Hsp60(wt)/Hsp10 or Hsp60-(p.Val98Ile)/Hsp10 operons |
Affymetrix Ecoli_ASv2 |
E-GEOD-10974 |
loaded 6/25/10 |
y |
|||
|
microarray |
Identification of the Escherichia coli HU regulon |
Affymetrix Ecoli_ASv2 |
E-GEOD-11183 |
loaded 6/26/10 |
||||
|
microarray |
Control of RpoS in global gene expression of Escherichia coli in minimal media |
Affymetrix Ecoli_ASv2 |
E-GEOD-12797 |
loaded 6/07/10 |
||||
|
microarray |
Gene expression of E. coli MG1655 at attachment, colony formation and maturation during biofilm formation |
Affymetrix Ecoli_ASv2 |
E-GEOD-13418 |
error: unknown file type (see notes) |
after gunzipping, .CEL and .dcp file types showed. | |||
|
microarray |
- |
E. coli MqsR and MqsA whole DNA microarray and nickel DNA enrichment microarray |
Affymetrix Ecoli_ASv2 |
E-GEOD-14203 |
||||
|
microarray |
Transcriptome Profiles For High-Cell-Density Recombinant and Wild-Type E. coli |
Affymetrix Ecoli_ASv2 |
E-GEOD-17505 |
|||||
|
microarray |
Serine hydroxamate and the transcriptome of high cell density recombinant E. coli MG1655 |
Affymetrix Ecoli_ASv2 |
E-GEOD-17506 |
|||||
|
microarray |
Global transcriptome response of recombinant E. coli to heat-shock and dual heat-shock recombinant protein induction |
Affymetrix Ecoli_ASv2 |
E-GEOD-17507 |
|||||
|
microarray |
Transcription profiling of LD13 mutant E. coli planktonic cultures and flow-cell biofilm after 24, 48, 72, 96 and 144 hours |
Affymetrix Ecoli_ASv2 |
E-MEXP-1408 |
|||||
|
microarray |
Molecular strategy for survival at a critical high temperature in Escherichia coli |
Affymetrix Ecoli_ASv2 |
E-MEXP-3191 |
|||||
|
microarray |
Transcription profiling of pNCF (non-conjugative factor of F plasmid) carrying E.coli biofilm |
Affymetrix Ecoli_ASv2 |
E-MEXP-1145 |
|||||
|
Transcription profiling of LD13 mutant E. coli planktonic cultures and flow-cell biofilm after 24, 48, 72, 96 and 144 hours |
Affymetrix Ecoli_ASv2 |
E-MEXP-1408 |
||||||
|
microarray |
Transcription profiling of E. coli F- phenocopies compared with K-12 young biofilm |
Affymetrix Ecoli_ASv2 |
E-MEXP-1001 |
|||||
|
microarray |
Aggarwal K and Lee KH (2011) J Bacteriol 193(18):4869-80 |
Overexpression of cloned RhsA sequences perturbs the cellular translational machinery in Escherichia coli. |
GSE12411 |
E-GEOD-12411 |
||||
|
microarray |
Transcription profiling of E. coli biofilm to assess the global gene impact of a natural F conjugative plasmid-carrying E.coli biofilm |
Affymetrix Ecoli_ASv2 |
E-MEXP-953 |
|||||
|
microarray |
Alteri CJ, et al. (2011) Mol Microbiol 82(1):145-63 |
The broadly conserved regulator PhoP links pathogen virulence and membrane potential in Escherichia coli. |
GSE3665 |
E-GEOD-3665 |
||||
|
microarray |
Transcription profiling of E. coli strains MG Kan N15(+), MG Kan-Tos N15(-) and MG Kan-Tos N15(+) which has a linear genome made by MG Kan N15(+) and MG Kan-Tos N15(-) |
Affymetrix Ecoli_ASv2 |
E-MEXP-910 |
|||||
|
microarray |
Comparative genomic hybridization of plasmids containing genomic library clones grown in E. coli to monitor copy number changes over time |
Affymetrix Ecoli_ASv2 |
E-TABM-143 |
|||||
|
microarray |
Transcription profiling of E. coli in two replicate series of 8 timepoints of exponential to stationary phase planktonic cultures growing in rich media |
Affymetrix Ecoli_ASv2 |
E-TABM-103 |
|||||
|
microarray |
E. coli treated with cefsulodin and mecillinam |
Affymetrix E_coli_2 and Ecoli_ASv2 |
GSE10159 (Affy_2) samples were loaded 2/6/10. |
This GSE accession combines subseries GSE10158 (Affy_ASv2) and GSE10159 (Affy_2) | ||||
|
microarray |
Whole-transcriptome profiling revealed that wild-type SdiA reduced biofilm formation by repressing genes related to indole synthesis and curli synthesis compared to when no SdiA was expressed, while variant SdiA1E11 induced genes related to indole synthesis in comparison to wild-type SdiA. |
Affymetrix E_coli_2 |
||||||
|
microarray |
E. coli EHEC strain 86-24 and isogenic luxS::tet strain VS94 grown with various signaling molecules (100 uM AI-2, 30 uM AI-3, or 50 uM epinephrine) |
Affymetrix E_coli_2 |
loaded 2/10/2010 |
5/15/10 Need to double check that all the arrays are loaded. | ||||
|
microarray |
Asakura Y, et al. (2011) Nucleic Acids Res 39(20):9034-46 |
GSE21869 |
E-GEOD-21869 |
| ||||
| edit table |
</protect>
Platform/Print/Physical Array Designs
Different microarray/gene expression repositories use different terminologies for the physical design of an array.
- SMD: Prints
- GEO: Platforms
- ArrayExpress: Arrays
Each database also has their own accession for a particular type of array.
<protect>
| Source | Product | GEO | ArrayExpress | SMD | Notes |
|---|---|---|---|---|---|
|
Affymetrix |
|||||
|
Beckman 2F Schoolink lab | |||||
|
Affymetrix |
Affymetrix Ecoli_ASv2 |
||||
|
Khodursky Lab |
Khodursky Lab E. coli B 4290 ORFs Microarray |
PCR products from primer pairs from Sigma-Genosys spotted on glass slides | |||
|
Liao Lab |
JCL_Ecoli_1 |
||||
|
Conway lab |
ConwayLab_Ecoli_6041 features_v1 |
| |||
| edit table |
</protect>
References
See Help:References for how to manage references in EcoliWiki.
- ↑ Dong, T & Schellhorn, HE (2009) Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933. BMC Genomics 10 349 PubMed
- ↑ Caldara, M et al. (2006) The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. Microbiology (Reading, Engl.) 152 3343-54 PubMed
- ↑ Soini, J et al. (2008) Norvaline is accumulated after a down-shift of oxygen in Escherichia coli W3110. Microb. Cell Fact. 7 30 PubMed
- ↑ Shabala, L et al. (2009) Ion transport and osmotic adjustment in Escherichia coli in response to ionic and non-ionic osmotica. Environ. Microbiol. 11 137-48 PubMed
- ↑ 5.0 5.1 García-Contreras, R et al. (2008) Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes. PLoS ONE 3 e2394 PubMed
- ↑ Cardinale, CJ et al. (2008) Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science 320 935-8 PubMed
- ↑ Blanchard, JL et al. (2007) Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks. PLoS ONE 2 e1186 PubMed
- ↑ Li, Y & Zhang, Y (2007) PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli. Antimicrob. Agents Chemother. 51 2092-9 PubMed
- ↑ Lee, J et al. (2007) Enterohemorrhagic Escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin. Appl. Environ. Microbiol. 73 4100-9 PubMed
- ↑ Bansal, T et al. (2007) Differential effects of epinephrine, norepinephrine, and indole on Escherichia coli O157:H7 chemotaxis, colonization, and gene expression. Infect. Immun. 75 4597-607 PubMed
- ↑ Alper, H & Stephanopoulos, G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab. Eng. 9 258-67 PubMed
- ↑ Bansal, T et al. (2008) Temporal regulation of enterohemorrhagic Escherichia coli virulence mediated by autoinducer-2. Appl. Microbiol. Biotechnol. 78 811-9 PubMed
- ↑ 13.0 13.1 Hancock, V et al. (2008) Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. Mol. Genet. Genomics 279 523-34 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
- ↑ Isalan, M et al. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452 840-5 PubMed
- ↑ Zhu, K et al. (2009) Transcriptional regulation of membrane lipid homeostasis in Escherichia coli. J. Biol. Chem. 284 34880-8 PubMed
- ↑ Wang, X et al. (2009) Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms. ISME J 3 1164-79 PubMed
- ↑ Ito, A et al. (2009) Localized expression profiles of rpoS in Escherichia coli biofilms. Biotechnol. Bioeng. 103 975-83 PubMed
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- PortEco Microarray Pipeline
