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Items: 1 to 20 of 293

1.

RfaH counter-silences inhibition of transcript elongation by H-NS–StpA H-NS nucleoprotein filaments in pathogenic E. coli

(Submitter supplied) Expression of virulence genes in pathogenic E. coli is controlled in part by the transcription silencer H-NS and its paralogs (e.g., StpA), which sequester DNA in multi-kb nucleoprotein filaments to inhibit transcription initiation, elongation, or both. Some activators counter-silence initiation by displacing H-NS from promoters. How H-NS inhibition of elongation is overcome is not understood. In uropathogenic E. more...
Organism:
Escherichia coli; Escherichia coli CFT073
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL32598 GPL16085
97 Samples
Download data: BW
Series
Accession:
GSE212064
ID:
200212064
2.

Transcriptomic analysis of homoserine-evolved MG1655 strain (wild type) and of homoserine -treated wild type, mutant deleted for thrL and mutant bearing thrL* allele

(Submitter supplied) The growth of E. coli is inhibited by millimolar concentrations of L-homoserine, which may be problematic for the industrial production of this compound or for products derived from it. In this work, an adapted laboratory evolution (ALE) was applied, which resulted in the isolation of an E. coli strain at least 10-fold more tolerant to L-homoserine than the original (MG1655) strain. Only four genomic modifications were identified after genome sequencing of this evolved strain (designed 4E), including a 49 bp truncation starting from the codon stop of thrL and leading to a modified thrL locus carrying a thrL* allele encoding a 30 amino acids polypeptide, which is 9 amino acids more than the leader peptide encoded by thrL. more...
Organism:
Escherichia coli str. K-12 substr. MG1655; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL13359
24 Samples
Download data: TXT, XLSX
Series
Accession:
GSE206196
ID:
200206196
3.

YciR, a specific 3′-phosphodiesterases, plays a role in the pathogenesis of Uropathogenic Escherichia coli CFT073

(Submitter supplied) Uropathogenic Escherichia coli are a prevailing causation of urinary tract infections infections and characterized by recurrence and resistance to antibiotics due to their misuse, causing a large economic burden to individuals and countries. An early determinant of the pathogenicity of UPEC is its ability to form intracellular bacterial communities in the cytoplasm of bladder epithelial cells after its invasion for evading immune response. more...
Organism:
Escherichia coli CFT073
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20323
2 Samples
Download data: TXT
Series
Accession:
GSE189294
ID:
200189294
4.

The FimZ regulon of E. coli in the stationary phase

(Submitter supplied) To compare the transcriptional profiling of a FimZ-expressing strain or non-expressing strain in E. coli under stationary phase. For overexpression of fimZ gene was cloned into pBAD33 plasmid under control of the arabinose-inducible PBAD promoter, which was induced by addition of 0.2% arabinose. Goal was to determine the FimZ regulon in E. coli. Biological replicates: 2 replicates.
Organism:
Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. EDL933; Escherichia coli BW25113; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platform:
GPL13359
2 Samples
Download data: TXT
Series
Accession:
GSE181402
ID:
200181402
5.

Testing the impact of Type I Restriction Modification Systems on Gene Expression in Uropathogenic Escherichia coli

(Submitter supplied) Background: DNA methylation influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. The regulatory role of DNA methylation and other epigenetic marks also extends to virulence; both orphan methyltransferases and those from restriction modification systems (RMSs) have been co-opted to regulate virulence in many bacteria. However, functional characterisation of DNA methylation mediated by archetypal Type I RMSs remains limited. more...
Organism:
Escherichia coli UTI89; Escherichia coli str. K-12 substr. MG1655; Escherichia coli CFT073
Type:
Expression profiling by high throughput sequencing
7 related Platforms
64 Samples
Download data: XLSX
Series
Accession:
GSE165421
ID:
200165421
6.

The transcriptome of gadE, hdeA, or hdeD null strains compared to wild-type of E. coli under minimum medium conditions

(Submitter supplied) To compare transcriptional profiling of a gadE-, hdeA-, or hdeD- deficient strain to wild type in E. coli under minimum medium conditions. These genes are included in the GAD cluster genes, which are involved in the glutamic acid-dependent acid resistance (GAD) in E. coli. Goal was to determine the GadE, HdeA, or HdeD regulon in E. coli. Biological replicates: 2 replicates.
Organism:
Escherichia coli BW25113; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by array
Platform:
GPL13359
6 Samples
Download data: TXT
Series
Accession:
GSE178954
ID:
200178954
7.

Tailoring a global iron regulon to a uropathogen

(Submitter supplied) Pathogenicity islands and plasmids encode genes for pathogenesis of various Escherichia coli pathotypes.Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here we dissected aregulatory network directed by the conserved iron homeostasis regulator, Ferric Uptake Regulator (Fur), inuropathogenic E. more...
Organism:
Escherichia coli CFT073
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18955
19 Samples
Download data: TXT, WIG
Series
Accession:
GSE145424
ID:
200145424
8.

Comparison of gene expression profiles of uropathogenic Escherichia coli CFT073 after prolonged exposure to subinhibitory concentrations of different biocides

(Submitter supplied) Biocides are chemical compounds widely used in hospital settings for a variety of purposes, but mainly for disinfection. The chemical properties of a biocide, as well as the biocide concentration, influence which cellular targets are affected. Exposure of bacteria to residual concentrations of biocides could lead to development of increased resistance towards the biocide in use, as well as cross-resistance towards other antimicrobials, including antibiotics. more...
Organism:
Escherichia coli; Escherichia coli CFT073
Type:
Expression profiling by array
Platform:
GPL3154
15 Samples
Download data: CEL
Series
Accession:
GSE135556
ID:
200135556
9.

Expression data in Esherichia coli wild type and ∆dnaK

(Submitter supplied) We found that nemerous genes were up- or down regulated in ∆dnaK, including RpoS-regulated genes.
Organism:
Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platform:
GPL13360
4 Samples
Download data: TXT
Series
Accession:
GSE102347
ID:
200102347
10.

E. coli transcriptome-level alterations upon antimicrobial peptide exposure

(Submitter supplied) E. coli (P1645ec: a clinical isolate) was incubated with differing concentrations of antimicrobial peptides (all at 0.5X MBC)
Organism:
Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by array
Platform:
GPL13359
8 Samples
Download data: TXT
Series
Accession:
GSE116304
ID:
200116304
11.

In vivo transcriptome analysis of avian pathogenic Escherichia coli under the control of RstA/RstB two-component regulatory system

(Submitter supplied) APEC cause avian colibacillosis in poultry, characterized by the systematic infection, such as septicemia, airsacculitis, and pericarditis. APEC mainly use two-component regulatory systems (TCSs) to deal with the stressing environments in host during their infection. Whereas most TCSs in E.coli are well characterized, the characterization of RstA/RstB in APEC has not been thoroughly investigated. To understand the whole picture of RstA/RstB regulation, especially its role in virulence regulation, transcriptional analysis of the effect of rstAB deletion was performed in vivo. more...
Organism:
Escherichia coli O157:H7 str. Sakai; Escherichia coli APEC O2; Escherichia coli str. K-12 substr. MG1655; Escherichia coli CFT073; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL13359
6 Samples
Download data: TXT
Series
Accession:
GSE112421
ID:
200112421
12.

A HUS-associated STEC expressing a dicA transcriptional module is related to gene network dysregulation in Caco-2

(Submitter supplied) We conducted comparative gene co-expression network (GCN) analyses of two O113:H21 STEC strains: EH41, reference strain, isolated from hemolytic-uremic syndrome patient in Australia, and Ec472/01, isolated from cattle feces in Brazil. These strains were cultured in fresh or in Caco-2 cell conditioned media. GCN analyses were also accomplished for cultured Caco-2 cells exposed to EH41 or Ec472/01. Differential transcriptome profiles for EH41 and Ec472/01 were not significantly changed by exposure to fresh or Caco-2 conditioned media. more...
Organism:
Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655; Homo sapiens; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platforms:
GPL13359 GPL6480
32 Samples
Download data: TXT
Series
Accession:
GSE45979
ID:
200045979
13.

To compare the transcriptome of ompR null strains with wild-type strain of E. coli and S. Typhimurium during stress

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai; Escherichia coli CFT073; Escherichia coli O157:H7 str. EDL933; Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Type:
Expression profiling by array
Platforms:
GPL24239 GPL13359
19 Samples
Download data: TXT
Series
Accession:
GSE106630
ID:
200106630
14.

To compare the transcriptome of ompR null strains with wild-type strain of E. coli during acid or osmotic stress

(Submitter supplied) In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in E. coli responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. more...
Organism:
Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by array
Platform:
GPL13359
11 Samples
Download data: TXT, XLSX
Series
Accession:
GSE106628
ID:
200106628
15.

Insights on Osmotic Tolerance Mechanisms in Escherichia coli Gained from an rpoC Mutation

(Submitter supplied) Transcriptional analysis of rpoC K370_A396dup mutants for tolerance to sodium chloride
Organism:
Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platform:
GPL13360
8 Samples
Download data: GPR
Series
Accession:
GSE94342
ID:
200094342
16.

E. coli BW25113 azide treated vs untreated cells

(Submitter supplied) Transcriptional profiling of mid-log phase (OD600 ~ 0.8) E. coli BW25113 cells grown treated with 2 mM NaN3 for 10 minutes
Organism:
Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. EDL933; Escherichia coli O157:H7 str. Sakai; Escherichia coli K-12
Type:
Expression profiling by array
Platform:
GPL13360
2 Samples
Download data: TXT
Series
Accession:
GSE102322
ID:
200102322
17.

Transcriptional Changes in Escherichia coli Upon Treatment with (-)-Roemerine

(Submitter supplied) Transcriptional profiling of Escherichia coli TB1 cells under (-)-Roemerine treatment. The genome reprograming in the bacterial cells at transcription level was analyzed through treatment of the bacteria with plant-derived alkaloid, (-)-Roemerine, to elucidate the response of bacteria to the antibacterial drug.
Organism:
Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platform:
GPL13359
13 Samples
Download data: TXT
Series
Accession:
GSE80827
ID:
200080827
18.

Transcriptional alterations of virulence-associated genes in extended spectrum beta-lactamase (ESBL)-producing uropathogenic Escherichia coli during morphologic transitions induced by ineffective antibiotics

(Submitter supplied) The present study examines changes in global gene expression patterns and in virulence factor-associated genes in an extended spectrum beta-lactamase (ESBL)-producing UPEC (ESBL019) during the morphologic transitions induced by an ineffective antibiotic and in the presence of human primary bladder epithelial cells. The morphological shifts induced by ineffective antibiotics are associated with significant transcriptional virulence alterations in ESBL-producing UPEC, which may affect survival and persistence in the urinary tract.
Organism:
Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073
Type:
Expression profiling by array
Platform:
GPL13359
16 Samples
Download data: TXT
Series
Accession:
GSE99661
ID:
200099661
19.

LLQR E. coli ATCC 25922 vs wild-type E. coli ATCC 25922

(Submitter supplied) Global response to ciprofloxacin in low level quinolone resistant Escherichia coli: a shorter path to survival. Background: Bactericidal activity of quinolones in bacteria has been related to a combination of DNA fragmentation, ROS production and programmed dead cell systems. Subjacent molecular systems responsible for reduction of bactericidal effect in low-level quinolone resistance (LLQR) phenotypes remain to be clarified. more...
Organism:
Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655; Escherichia coli ATCC 25922; Escherichia coli O157:H7 str. Sakai; Escherichia coli CFT073
Type:
Expression profiling by array
Platform:
GPL13360
8 Samples
Download data: TXT, XLSX
Series
Accession:
GSE86341
ID:
200086341
20.

Global gene expression profiling and antibiotic susceptibility after repeated exposure to the carbon monoxide-releasing molecule-2 (CORM-2) in multidrug-resistant ESBL-producing uropathogenic Escherichia coli

(Submitter supplied) Treatment of urinary tract infections is today a challenge due to the increasing prevalence of multidrug-resistant ESBL-producing uropathogenic Escherichia coli (UPEC). There is an urgent need for new treatment strategies for multidrug-resistant UPEC and preferably with targets that have low potential for development of resistance. Carbon monoxide-releasing molecules (CORMs) are novel and potent antibacterial agents. more...
Organism:
Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. Sakai; Escherichia coli CFT073
Type:
Expression profiling by array
Platform:
GPL13359
16 Samples
Download data: TXT
Series
Accession:
GSE87627
ID:
200087627
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