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Items: 1 to 20 of 151

1.

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
2.

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; 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
16 Samples
Download data: TXT
Series
Accession:
GSE99661
ID:
200099661
3.

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

(Submitter supplied) While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. more...
Organism:
Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL23073
4 Samples
Download data: XLSX
4.

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 CFT073; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platform:
GPL13360
8 Samples
Download data: TXT, XLSX
Series
Accession:
GSE86341
ID:
200086341
5.

RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933

(Submitter supplied) In order to define the role of H-NS in regulating gene transcription and further find out the biological significance of this protein in EHEC, we conducted RNA-seq and then analyzed the transcriptome data, using EHEC O157:H7 strain EDL933 and Δhns. A total of 983 genes were found to be regulated by H-NS. 213 and 770 genes exhibited lower and higher transcript levels in Δhns than in WT, respectively. more...
Organism:
Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21021
4 Samples
Download data: XLSX
Series
Accession:
GSE73969
ID:
200073969
6.

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 CFT073; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platform:
GPL13359
16 Samples
Download data: TXT
Series
Accession:
GSE87627
ID:
200087627
7.

Escherichia coli: untreated versus 5-azacytidine-treated expression profiles

(Submitter supplied) DNA microarray experiments were used to compare gene expression profiles of untreated and 5-azacytidine treated Escherichia coli at both logarithmic phase and early stationary phase The goal was to determine the effect of cytosine DNA methylation loss on gene expression (5-azacytidine is a methylation inhibitor)
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:
GPL13360
10 Samples
Download data: TXT
Series
Accession:
GSE73707
ID:
200073707
8.

Enterococcus faecalis downregulates virulence genes of EHEC

(Submitter supplied) The transcriptome of EHEC grown in vitro with or without Symbioflor® was analyzed using RNA-seq. The analysis revealed downregulation of several virulence-associated genes in the presence of Symbioflor®, including virulence key genes (e.g., LEE, flagellum, quorum-sensing).
Organism:
Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22365
2 Samples
Download data: XLSX
Series
Accession:
GSE85950
ID:
200085950
9.

Transcriptomic changes of Escherichia coli expressing BnTR1 at normal and heat stress conditions

(Submitter supplied) The heat shock response is critical for organisms to survive at a high temperature. Heterologous expression of eukaryotic molecular chaperons protects Escherichia coli against heat stress. Here we report that expression of the plant E3 ligase BnTR1 significantly increase the thermotolerance of Escherichia coli. Different from eukaryotic chaperones, BnTR1 post-transcriptionally regulates the heat shock factor σ32 though zinc fingers of the RING domain, which interacts with DnaK resulting in stabilizing σ32 and subsequently up-regulating heat shock proteins. more...
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:
GPL13360
12 Samples
Download data: TXT
Series
Accession:
GSE85807
ID:
200085807
10.

DNA Microarray of Global Transcription Factor Mutant Reveals Membrane-Related Proteins Involved in n-Butanol Tolerance in Escherichia coli

(Submitter supplied) We successfully isolated an E. coli strain harboring rpoD mutant B8 with 2% (v/v) butanol tolerance using global transcriptional machinery engineering approach. DNA microarrays were employed to assess the transcriptome profile of n-butanol tolerance strain B8 and control strain E. coli JM109. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.
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
6 Samples
Download data: TXT
Series
Accession:
GSE79305
ID:
200079305
11.

Enterohemorrhagic Escherichia coli: impact of short chain fatty acid treatment on virulence gene expression

(Submitter supplied) transcriptome analysis of enterohemorrhagic E. coli treated with either one of two different concentrations of short chain fatty acid mixes or the corresponding sodium chloride osmolarity control
Organism:
Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL13359
6 Samples
Download data: TXT
Series
Accession:
GSE79509
ID:
200079509
12.

Ginkgolic acids and Ginko biloba extract inhibit Escherichia coli O157:H7 biofilm formation

(Submitter supplied) Contamination with enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a worldwide problem but there is no effective therapy available for EHEC infection. Biofilm formation is closely related with EHEC infection and is one of the mechanisms of antimicrobial resistance. Antibiofilm screening of 560 plant secondary metabolites against EHEC shows that ginkgolic acids C15:1 and C17:1 at 5 μg/ml and Ginko biloba extract at 100 μg/ml significantly inhibited EHEC biofilm formation on the surface of polystyrene, nylon membrane, and glass. more...
Organism:
Escherichia coli; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL3154
2 Samples
Download data: CEL, CHP, XLS
Series
Accession:
GSE49367
ID:
200049367
13.

Transcriptomic analysis of glycolaldehyde-treated wild type cells and a synthetic strain

(Submitter supplied) A synthetic pathway for (D)-xylose assimilation was stoichiometrically evaluated regarding its potential to produce selected value-added compounds and implemented in Escherichia coli strains. The pathway proceeds via the isomerization of (D)-xylose to (D)-xylulose, the phosphorylation of (D)-xylulose to obtain (D)-xylulose-1-phosphate (Xyl1P), and the aldolase cleavage of the latter to yield glycolaldehyde and DHAP. more...
Organism:
Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL13360
9 Samples
Download data: TXT
Series
Accession:
GSE69265
ID:
200069265
14.

Expression profiling of EvgSc and ompR mutants

(Submitter supplied) In order to explore the transcriptional reprogramming in EvgSc, ompR and EvgSc/ompR mutants we have used whole genome microarray profiling.
Organism:
Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL13360
8 Samples
Download data: TXT
Series
Accession:
GSE56833
ID:
200056833
15.

Escherichia coli K-12: 0%, 10% and 30% hydrogen peroxide (H2O2) treatments, in wild type and luxS mutants

(Submitter supplied) Transcripitonal profiling of Escherichia coli K-12 W3110 comparing wild type and luxS mutants without or with 10%, 30% H2O2 treatments, two biological replicates for each condition
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:
GPL13360
6 Samples
Download data: TXT
Series
Accession:
GSE38186
ID:
200038186
16.

Control of the E. coli SOS regulon expression by intracellular dNTP pool changes

(Submitter supplied) We studied SOS mutator effect mediated by recA730 and changes in the dNTP pool. We found that established dNTP pool changes resulting from deficiencies in the ndk or dcd genes, had a strongly suppressive effect on the recA730 mutator effect. To investigate whether the observed reduction in SOS mutator effect is due to lowered expression of the entire SOS regulon, we performed microarray analysis of gene expression profiles in each of the single ndk, dcd, and recA730 strains, as well as the double recA730 ndk and recA730 dcd strains.
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
5 Samples
Download data: TXT
Series
Accession:
GSE62898
ID:
200062898
17.

Expression profiling of E. coli expressing the heterologous sigma70 factor (rpoD) of Lactobacillus plantarum

(Submitter supplied) Time course experiment to analyze transcriptional changes to the E. coli transcriptome due to overexpressing the heterologous sigma70 factor (RpoD) of Lactobacillus plantarum. A plasmid control strain (pControl) and the sigma70 overexpression strain (pLPLσ) were cultivated in parallel and after induction of RpoD expression samples for transcriptional profiling were taken in exponential, transition and stationary phase.
Organism:
Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli O157:H7 str. EDL933; Escherichia coli str. K-12 substr. MG1655; Escherichia coli
Type:
Expression profiling by array
Platform:
GPL13360
12 Samples
Download data: TXT
Series
Accession:
GSE66995
ID:
200066995
18.

Comparison between wild type E. coli and adhE (alcohol dehydrogenase) mutants, grown under anaerobic condition

(Submitter supplied) To characterize anaerobic stress-induced expression in adhE mutants, the microarray experiment was performed with two serotypes of wild type E. coli and their adhE mutants: (1) K-12 strain, wild type; (2) B strain, wild type; (3) BW25113, adhE mutants; (4) BL21(DE3), adhE mutants. Under anaerobic growth condition in glucose-containing complex medium, the wild type strains 1 and 2 grew well whereas the mutant strains 3 and 4 experienced anaerobic stress and grew after 24 hours and 48 hours, respectively.
Organism:
Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli BL21(DE3); Escherichia coli str. K-12 substr. MG1655; Escherichia coli BW25113; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL13359
4 Samples
Download data: TXT
Series
Accession:
GSE46455
ID:
200046455
19.

Escherichia coli K-12: 5% isooctane treatment at four time points

(Submitter supplied) Transcripitonal profiling of Escherichia coli K-12 BW25113 comparing cells with isooctane treatment at time point of 0, 10, 30 and 60 min with two biological replicates
Organism:
Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655; Escherichia coli K-12; Escherichia coli O157:H7 str. EDL933
Type:
Expression profiling by array
Platform:
GPL13360
4 Samples
Download data: TXT
Series
Accession:
GSE32131
ID:
200032131
20.

Effect of Titanium dioxide nanoparticles on Escherichia coli K12 MG1655 genes expression

(Submitter supplied) In the present study, we investigated the transcriptional expression patterns of the model strain E. coli exposed to titanium dioxide nanoparticles (NP-TiO2), under dark conditions by using a microarray. Expression profiles were compared to unexposed E.coli and ratio of expression were analysed.
Organism:
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
8 Samples
Download data: TXT
Series
Accession:
GSE55972
ID:
200055972
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