GEO DataSets

(Submitter supplied) OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently, OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. more...

Organism:

Escherichia coli K-12; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Genome binding/occupancy profiling by array

Platforms:

GPL10008 GPL17580

21 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and ompR mutant grown to mil-exponential phase in LB. The goal was to define the ompR-regulated genes.

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platform:

GPL5780

8 Samples

Download data: GPR

(Submitter supplied) We have shown that mitomycin C induces expression of the rsr-yrlBA-rtcBA operon in Salmonella Typhimurium in a manner that is dependent on the activator for this operon, RtcR. As such, treatment with mitomycin C generates the ligand or other cellular conditions that activate RtcR and likely generates the substrates on which the components of this RNA repair operon act. We performed an RNA-seq analysis on WT cells and cells with components of the RNA repair operon, or the activator of the operon, deleted with and without mitomycin C. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21220

24 Samples

Download data: XLSX

(Submitter supplied) Comparisons of overexpression of PreA (in wt or preAB mutant Salmonella) to Salmonella lacking preA or preAB in late log phase growth in LB

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL3788

12 Samples

Download data

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

Organism:

Escherichia coli O157:H7 str. Sakai; Escherichia coli CFT073; Escherichia coli O157:H7 str. EDL933; Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platforms:

GPL24239 GPL13359

19 Samples

Download data: TXT

(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 S. Typhimurium 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:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by array

Platform:

GPL24239

8 Samples

Download data: TXT, XLSX

(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 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:

GPL13359

11 Samples

Download data: TXT, XLSX

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

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

Platform:

GPL17439

6 Samples

Download data: GFF

(Submitter supplied) A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17439

4 Samples

Download data: CSV

(Submitter supplied) A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17439

2 Samples

Download data: GFF

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

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL9091 GPL5780

40 Samples

Download data: GPR, TXT

(Submitter supplied) We used ChIP-chip analysis to identify where the nucleoid associated protein StpA binds on the Salmonella Typhimurium genome. We identified 285 chromosomal regions bound by StpA, ranging in size from 400 to 3500 base pairs and containing 572 genes. Comparison of the ChIP data revealed that StpA displayed an identical binding profile to H-NS; all genomic regions associated with StpA were also bound by H-NS. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5791

8 Samples

Download data: TXT

(Submitter supplied) StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL9091

12 Samples

Download data: GPR

(Submitter supplied) StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. more...

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platforms:

GPL5780 GPL9091

28 Samples

Download data: GPR, TXT

(Submitter supplied) Salmonella enterica var. Typhimurium (S. Typhimurium) is a Gram-negative, facultative intracellular pathogen that infects the intestinal tracts of humans and animals. In the host, S. Typhimurium encounters a wide range of oxygen concentrations going from oxic conditions in the stomach to near anoxic conditions in the distal sigmoid colon-rectal junction. In Escherichia coli, FNR (Fumarate Nitrate Reductase) is one of the main regulatory proteins involved in oxygen sensing and in controlling the transcription of the genes required for the aerobic/anaerobic transition.. more...

Organism:

Salmonella; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL1835

6 Samples

Download data

(Submitter supplied) Culture was split into halves and 500 uM dipyridyl was added to one half. Samples were collected after the indicated times. Groups of assays that are related as part of a time series. Keywords: time_series_design

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL3048

6 Samples

Download data

(Submitter supplied) The regulon of genes controlled by the HU nucleoid-associated proteins was examined in Salmonella enterica serovar Typhimurium (S. Typhimurium). DNA microarrays were used to detect the effect on the bacterial transcriptome of knockout mutations in the hupA, the hupB and in both the hupA and hupB genes. Distinct but overlapping patterns of gene expression were detected in the transcriptome at each time point for each of the three mutants, pointing to the existence of not one but three regulons of genes controlled by the HU proteins. more...

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL9091

37 Samples

Download data: GPR

(Submitter supplied) Environmental stress contributes to the outcome of infection by impacting both microbial virulence and host susceptibility to infection. Thermal processing, commonly used for decontamination of poultry in the food industry, may elicit sublethal stress on resistant serovars of Salmonella. We employed traditional heat shock temperatures (42 and 48ºC), similar to avian body temperature and poultry processing conditions, to study gene expression of Salmonella enterica serovar Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL9181

12 Samples

Download data: GPR

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

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

Platform:

GPL20056

21 Samples

Download data: BW

(Submitter supplied) The Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect of rewiring the Fis regulatory network in Salmonella by moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the Right macrodomain of the chromosome, creating the strain GX. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

12 Samples

Download data: BW, XLSX