GEO DataSets

(Submitter supplied) The first goal of the study was to identify genes differentially regulated by MavR in EHEC strain 86-24. The second goal was to identify direct targets of MavR through the MAPS protocol.

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29711 GPL28511

10 Samples

Download data: TXT

(Submitter supplied) Bacterial pathogens must be able to both recognize suitable niches within the host for colonization and successfully compete with commensal flora for nutrients in order to establish infection. Ethanolamine (EA) is a major component of mammalian and bacterial membranes and may be used by pathogens as a carbon and/or nitrogen source in the gastrointestinal tract. We examined how EA influences gene expression in the human pathogen enterohemorrhagic Escherichia coli O157:H7 (EHEC). more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) sRNAs play important roles in regulating gene expression post-transcriptionally. Here, we used RNA-seq to compare gene expression in a WT strain and a dicF1-4 deletion strain.

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24005

6 Samples

Download data: TXT

(Submitter supplied) Enteric pathogens with low infectious doses rely on the ability to orchestrate expression of virulence and metabolism-associated genes in response to environmental cues for successful infection. Accordingly, the human pathogen enterohemorrhagic Escherichia coli (EHEC) employs a complex multifaceted regulatory network to link expression of type III secretion system (T3SS) factors to nutrient availability. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24005

6 Samples

Download data: TXT

(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

(Submitter supplied) Previous experiments have shown that E. feacalis increases EHEC virulence by secreting adenine, this RNAseq aims to understand the molecular mechanism underlaying adenine role on EHEC

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

20 Samples

Download data: TXT

(Submitter supplied) Previous experiments have shown that E. feacalis increases EHEC virulence, this RNAseq aims to understand the molecular mechanism underlaying this phenotype

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

6 Samples

Download data: TAB

(Submitter supplied) Analysis of effect of deletion of the two adrenergic kinases QseC and QseE on gene expression of EHEC 8624 in the absence and presence of epinephrine

Organism:

Escherichia coli; Escherichia coli O157:H7

Type:

Expression profiling by array

Platform:

GPL3154

8 Samples

Download data: CEL, CHP

(Submitter supplied) Role of L-arabinose on gene expression in E. coli O157:H7 TUV93-0 where CTRL samples were grown in the absence of L-arabinose and ARA samples were grown in the presence of L-arabinose.

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34321

6 Samples

Download data: TXT

(Submitter supplied) Escherichia coli O157:H7 is a food-borne pathogen that causes bloody diarrhea and hemolytic uremic syndrome. Hfq is an sRNA chaperone protein that is involved in post-transcriptional regulation of virulence genes in pathogenic bacteria. In EHEC strain EDL933, Hfq acts a negative regulator of the locus of enterocyte effacement (LEE) that encodes most of the proteins involved in type three secretion and attaching and effacing lesions. more...

Organism:

Escherichia coli O157:H7; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) Analysis of effect of deletion of the two transcriptional factors KdpE and Cra on gene expression of EHEC 8624

Organism:

Escherichia coli 8624; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

3 Samples

Download data: CEL, CHP

(Submitter supplied) Fimbriae are important virulence traits that promote bacterial adhernece to surfaces. Here, we assessed whether fimbriae modulate gene expression using microarrays. We used microarrays to compare gene expression in wild-type of fimbrial deletion strains of EHEC

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

3 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24659 GPL26592

30 Samples

Download data: FA, GTF

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL24659

16 Samples

Download data: TXT

(Submitter supplied) By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

14 Samples

Download data: XLSX

(Submitter supplied) Transcriptional analysis of the effects of the deletion of the sRNAs glmY and glmZ in EHEC

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

3 Samples

Download data: CEL, CHP

(Submitter supplied) The goals of this experiment was to obtain a transcriptional profile of EHEC 86-24 upon deletion of fusK or fusR genes.

Organism:

Escherichia coli; Escherichia coli O157:H7

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) In many gram-negative and some gram-positive bacteria small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism, and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA-mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3'-to-5' exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL15010

12 Samples

Download data: TXT, XLSX

(Submitter supplied) VS94 gene expression at different time-points in SAPI medium in absence and presence of AI-2 was studied. Autoinducer-2 (AI-2) is produced by many species of bacteria, including various commensal bacteria and is involved in inter-species communication. Since, pathogens encounter AI-2 once they enter the human gastro-intestinal tract; we studied the effects of presence of AI-2 on various phenotypes associated with infection and colonization of enterohemorrhagic Escherichia coli (EHEC) namely, chemotaxis, motility and attachment to HeLa cells. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

8 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: GPR, GTF, TXT