Similar studies for GEO DataSets (Select 200018424) - GEO DataSets

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Items: 14

Select item 2000184241.

The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium

(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

Series

Accession:: GSE18424

ID:: 200018424

Select item 2000184522.

Role of stpA in Salmonella typhimurium

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

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

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

Platforms:: GPL9091 GPL5780
40 Samples

Download data: GPR, TXT

Series

Accession:: GSE18452

ID:: 200018452

Select item 2000184503.

Identification of StpA-binding sites on the Salmonella genome

(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

Series

Accession:: GSE18450

ID:: 200018450

Select item 2000184284.

StpA prevents RpoS-dependent transcription during mid-exponential growth in S. Typhimurium

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

Type:: Expression profiling by array

Platform:: GPL9091
12 Samples

Download data: GPR

Series

Accession:: GSE18428

ID:: 200018428

Select item 2002120645.

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

PubMed Full text in PMC Similar studies

Select item 2000522356.

Gene expression analysis of Salmonella enterica serovar Typhimurium strain SL1344 swap

(Submitter supplied) We performed transcriptome abundance analysis of Salmonella Typhimurium strain SL1344 swap which has been genetically engineered to express the hns open-reading frame from the stpA promoter and the stpA open reading frame from the hns promoter. This strain is designated SL1344(swap). Transcript abundance was compared with that of wild-type SL1344. This comparison was performed to determine the effect of chromosome location of the expression of two related global regulators and how alterations to their expression patterns would impact on their regulons.

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

Type:: Expression profiling by array

Platform:: GPL10008
6 Samples

Download data: GPR

Series

Accession:: GSE52235

ID:: 200052235

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000127977.

Control of RpoS in global gene expression of Escherichia coli in minimal media

(Submitter supplied) RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli. The RpoS regulon expression has been well characterized in rich media that support fast growth and high growth yields. In contrast, though RpoS levels are high in minimal media, how RpoS functions under such conditions has not been clearly resolved. In this study, we compared the global transcriptional profiles of wild type and an rpoS mutant of E. more...

Organism:: Escherichia coli K-12

Type:: Expression profiling by array

Platform:: GPL199
12 Samples

Download data: CEL, CHP

Series

Accession:: GSE12797

ID:: 200012797

Select item 2000200958.

Antagonistic regulation of motility and other cellular functions by RpoN and RpoS in Escherichia coli

(Submitter supplied) Bacteria generally possess multiple σ factors that, based on structural and functional similarity, divide into two families: σD and σN. Among the seven σ factors in Escherichia coli, six belongs to the σD family. Each σ factor recognizes a group of promoters, providing effective control of differential gene expression. Many studies have shown that σ factors of the σD family compete with each other for function. more...

Organism:: Escherichia coli; Escherichia coli K-12

Type:: Expression profiling by array

Platform:: GPL3154
9 Samples

Download data: CEL, CHP

Series

Accession:: GSE20095

ID:: 200020095

Select item 2000499149.

ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 μg/ml)

(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

Series

Accession:: GSE49914

ID:: 200049914

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20006711910.

Polyamines induce the glutamate decarboxylase acid response system by increasing the level of the σ38 subunit (RpoS) of Escherichia coli RNA polymerase via gadE regulon

(Submitter supplied) To study the physiological roles of polyamines, we have carried out a global microarray analysis on the effect of adding polyamines to an Escherichia coli mutant that lacks polyamines because of deletions in the genes in the polyamine biosynthetic pathway. Previously, we have reported that the earliest response to the polyamine addition is the increased expression of the genes for the glutamate dependent acid resistance system (GDAR). more...

Organism:: Escherichia coli

Type:: Expression profiling by array

Platform:: GPL3154
24 Samples

Download data: CEL

Series

Accession:: GSE67119

ID:: 200067119

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20011996711.

Experimental promoter identification of a representative food-borne pathogen Salmonella enterica serovar Typhimurium LT2 with near single base-pair resolution

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

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli str. K-12 substr. MG1655

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

Platforms:: GPL17439 GPL22503
10 Samples

Download data: GFF

Series

Accession:: GSE119967

ID:: 200119967

PubMed Full text in PMC Similar studies

Select item 20011996612.

Experimental promoter identification of a representative food-borne pathogen Salmonella enterica serovar Typhimurium LT2 with near single base-pair resolution (RNA-seq)

(Submitter supplied) RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:: Expression profiling by high throughput sequencing

Platform:: GPL22503
2 Samples

Download data: GFF, TXT

Series

Accession:: GSE119966

ID:: 200119966

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011996513.

Experimental promoter identification of a representative food-borne pathogen Salmonella enterica serovar Typhimurium LT2 with near single base-pair resolution

(Submitter supplied) RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

Organism:: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli str. K-12 substr. MG1655

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL17439 GPL22503
8 Samples

Download data: GFF

Series

Accession:: GSE119965

ID:: 200119965

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20010513314.

Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq

(Submitter supplied) Bacterial genomes encode in many instances more than one copy of genes coding for global modulators. In the Enterobacteriaceae, cells express the global modulator H-NS and its paralogue StpA. The enteroaggregative E. coli strain 042 encodes, in addition to the hns and stpA genes, an additional hns gene. We used RNA-seq to compare the transcriptome of the wt strain and its hns, hns2 and double hns hns2 derivatives, as well as of an hha null mutant (hhahha2). more...