GEO DataSets

(Submitter supplied) An experiment to test the equivalence of the Citrobacter rodentium RegA and E.Coli SMS 3-5 homologue

Organism:

Citrobacter rodentium

Type:

Expression profiling by array

Platform:

GPL7345

16 Samples

Download data: TXT

(Submitter supplied) Identification of the targets of RegA with and without bicarbonate stimulation by comparing RegA knockout to multicopy RegA transgenics. RegA is an AraC like transcription factor identified in a mutational screen for virulence genes in Citrobacter rodentium, an attaching and effacing pathogen that causes transmissible colonic hyperplasia in mice. This experiment compares the RegA null strain with a multicopy plasmid rescue of this null strain in the presence and absence of bicarbonate with the aim of identifying pathogenesis related genes related to the early and late stages of attachment and effacement. more...

Organism:

Citrobacter rodentium

Type:

Expression profiling by array

Platform:

GPL7345

8 Samples

Download data: TXT

(Submitter supplied) In Situ synthesis

Organism:

Citrobacter rodentium

3 Series

40 Samples

Download data

(Submitter supplied) RNA seq experiment was perfomed in the presence and absence of 500uM indole

Organism:

Escherichia coli O157:H7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25528

4 Samples

Download data: ASTAR, TXT

(Submitter supplied) To investigate the regulatory targets of the RegR virulence regulon of rabbit specific enteropathogenic Escherichia coli strain E22

Organism:

Escherichia coli E22

Type:

Expression profiling by array

Platform:

GPL16094

8 Samples

Download data: TXT

(Submitter supplied) Citrobacter rodentium is a murine pathogen used to model the intestinal infection caused by Enteropathogenic and Enterohemorrhagic Escherichia coli (EPEC and EHEC), two diarrheal pathogens responsible for morbidity and mortality in developing and developed countries, respectively. During infection, these bacteria must sense and adapt to the gut environment of the host. In order to adapt to changing environmental cues and modulate expression of specific genes, bacteria can use two-component signal transduction systems (TCS). more...

Organism:

Citrobacter rodentium

Type:

Expression profiling by array

Platform:

GPL25012

12 Samples

Download data: TXT

(Submitter supplied) RNA seq experiment was perfomed in the presence and absence of 10µM serotonin

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

2 Samples

Download data: ASTAR, XLSX

(Submitter supplied) to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA and phoB mutants when grown in phosphate-rich and phosphate-low medium

Organism:

Citrobacter rodentium

Type:

Expression profiling by array

Platform:

GPL7345

16 Samples

Download data: TXT

(Submitter supplied) Homeostatic interactions between the host and its resident microbiota is important for normal physiological functions and if altered, it could lead to dysbiosis, a change in the structure and function of the microbiota, and as a result to various pathophysiologies. Altered structure in bacterial community is associated with various pathophysiologies, but we are just beginning to understand how these structural changes translate into functional changes. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

11 Samples

Download data: CEL

(Submitter supplied) Whole genome trancription study of Citrobacter rodentium grown in rich media. Publication Title: Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux Publication Author List: Nicola K. Petty, Theresa Feltwell, Derek Pickard, Simon Clare, Ana L. Toribio, Maria Fookes, Kevin Roberts, Rita Monson, Satheesh Nair, Robert A. Kingsley, Richard Bulgin, Siouxsie Wiles, David Goulding, Craig Corton, Nicola Lennard, David Harris, David Willey, Richard Rance, Lu Yu, Jyoti S. more...

Organism:

Citrobacter rodentium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13894

2 Samples

Download data

(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) To gain mechanistic insights into this phenomenon, we characterized the regulatory role of Rnr in the virulence of prototype EPEC strain E2348-69 by genetic, biochemical, and human organoid-based approaches. Accordingly, RNA-seq analysis revealed more than 500 genes differentially regulated by Rnr, including the type-3 secretion system (T3SS).

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: XLSX

(Submitter supplied) Investigation of whole genome gene expression level changes in a B. suis 1330 regA mutant, compared to the wild-type strain. The two-component system RegBA of Brucella suis plays a central role in the control of respiratory systems adapted to oxygen deficiency. The mutant strain is affected in long-term persistence in vitro (this study) and in chronic infection in vivo (Abdou, E et al. 2013, Infect.Immun. more...

Organism:

Brucella suis; Brucella suis 1330

Type:

Expression profiling by array

Platform:

GPL22261

6 Samples

Download data: CALLS, PAIR

(Submitter supplied) Enterohaemorrhagic E. coli is significant human pathogen that causes disease ranging from haemorrhagic colitis to haemolytic uremic syndrome. The later can lead to potentially fatal renal failure and is caused by the release of Shiga toxins that are encoded within lambdoid bacteriophages. The toxins are encoded within the late transcript of the phage and are regulated by anti-termination of the PR’ late promoter during lytic induction of the phage. more...

Organism:

Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28004

8 Samples

Download data: BEDGRAPH, SGR

(Submitter supplied) UV-crosslining of protein-RNA complexes was employed to capture sRNA-mRNA interactions occuring on the RNA degradosome protein, RNase E, in enterohaemorhaggic E. coli. Abstract from associated mansucript: In many organisms small regulatory RNAs (sRNA) play important roles in the regulation of gene expression by base-pairing to specific target mRNAs. In enterohaemorrhagic E. coli (EHEC), sRNAs are encoded by both the “core” genome and in numerous horizontally acquired pathogenicity islands. more...

Organism:

Escherichia coli O157:H7 str. Sakai

Type:

Other

Platform:

GPL21393

2 Samples

Download data: GTF, HYB

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

Organism:

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

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: GPR, GTF, TXT

(Submitter supplied) UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additionally crosslinked Hfq in non-pathogenic E. coli K12 str. MG1655 grown in LE media. Hfq-RNA complexes were purified and trimmed using RNase A/T1. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17026 GPL17025 GPL17024

11 Samples

Download data: GTF

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

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL16085 GPL17439

16 Samples

Download data: GFF

(Submitter supplied) The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16085

8 Samples

Download data: CSV

(Submitter supplied) The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17439

8 Samples

Download data: GFF