GEO DataSets

(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

(Submitter supplied) RpoS is a conserved stress regulator that plays a critical role in survival under stress conditions in Escherichia coli and other γ-proteobacteria. RpoS is also involved in virulence of many pathogens including Salmonella and Vibrio species. Though well characterized in non-pathogenic E. coli K12 strains, the effect of RpoS on transcriptome expression has not been examined in pathogenic isolates. E. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL

(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

(Submitter supplied) This study is to identify the RpoS regulon in MG1655 in early exponential growth. RNA samples from wild type or rpoS mutants were extracted using acidic hot phenol method and hybridized to Affymetrix E. coli Antisense Genome Array. Keywords: Define regulon of RpoS

Organism:

Escherichia coli K-12

Type:

Expression profiling by array

Dataset:

GDS3123

Platform:

GPL199

6 Samples

Download data: CEL, CHP

Analysis of rpoS knockout mutants of bacteria K-12 strain MG1655 cells in exponential phase. RpoS, an alternative sigma factor and a stress response regulator, is a major regulator of genes required for stationary phase adaptation. Results provide insight into the role of RpoS in exponential phase.

Organism:

Escherichia coli K-12

Type:

Expression profiling by array, transformed count, 2 strain sets

Platform:

GPL199

Series:

GSE9814

6 Samples

Download data: CEL, CHP

(Submitter supplied) We varied RpoS levels using a mutation or an arabinose-inducible RpoS construct during stationary phase in rich media. We then sequenced cDNA from three separate RpoS levels, corresponding to 0%, 26% and 100% of wild-type levels.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

6 Samples

Download data: GFF, TXT

(Submitter supplied) The faecal indicator bacterium Escherichia coli K12 was used to study the effects of the global regulators RpoS and cAMP at the transcription level using microarray technology during short-term (physiological) adaptation to slow growth under limited nutrient supply. Effects due to the absence of one global regulator were assessed by comparing the mRNA levels isolated from rpoS or cya mutants under glucose-limited continuous culture at a dilution rate of 0.3 h-1 for the rpoS mutant or 0.16 h-1 for the cya mutant with those from wt E. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

6 Samples

Download data

(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

(Submitter supplied) Because many virulence genes in E. coli and other pathogens are regulated by temperature, we wanted to determine on a genome-wide scale which genes are modulated in adapting to both human host temperature (37˚C) and ambient room temperature (23˚C). Overall, 126 genes were found to be more highly expressed at 37˚C (1) whereas 297 genes were more highly expressed at 23˚C (2). Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the 37˚C list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL5942

5 Samples

Download data: GPR, TXT

(Submitter supplied) The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

18 Samples

Download data: CEL

(Submitter supplied) Transcription profiling of wild type, relA-, and relA-spoT-, crp-, dksA-, rpoS-, lrp- mutant strains of E. coli starved for isoleucine Bacteria comprehensively reorganize their global gene expression when faced with nutrient exhaustion. In Escherichia coli and other free-living bacteria, the alarmone ppGpp facilitates this massive response by directly or indirectly coordinating the down-regulation of genes of the translation apparatus, and the induction of biosynthetic genes and the general stress response. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933; Enterococcus faecalis V583; Bacillus anthracis; Escherichia coli CFT073; Bacteroides thetaiotaomicron VPI-5482; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platforms:

GPL3154 GPL6702

30 Samples

Download data: CEL, TXT

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

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; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

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 subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica

Type:

Expression profiling by array

Platforms:

GPL9091 GPL5780

28 Samples

Download data: GPR, TXT

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

Organism:

Pseudomonas protegens Pf-5; Pseudomonas protegens

Type:

Expression profiling by array

Platforms:

GPL7621 GPL7620

18 Samples

Download data: MEV, TXT

(Submitter supplied) Transcriptomic profiling of an rpoS mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown in nutrient broth supplemented with 1% glycerol to OD600=2.0-2.4 (early stationary phase).

Organism:

Pseudomonas protegens Pf-5; Pseudomonas protegens

Type:

Expression profiling by array

Platform:

GPL7620

6 Samples

Download data: TXT

(Submitter supplied) Transcriptomic profiling of an rpoS mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown on pea seed surfaces for 24h.

Organism:

Pseudomonas protegens; Pseudomonas protegens Pf-5

Type:

Expression profiling by array

Platform:

GPL7621

6 Samples

Download data: MEV, TXT

(Submitter supplied) Transcriptomic profiling of a gacA mutant of Pseudomonas protegens Pf-5 in comparison to the wild-type Pf-5 strain grown on pea seed surfaces for 24h.

Organism:

Pseudomonas protegens; Pseudomonas protegens Pf-5

Type:

Expression profiling by array

Platform:

GPL7621

6 Samples

Download data: MEV, TXT

(Submitter supplied) The RpoS sigma factor protein of Escherichia coli is the master transcriptional regulator of physiological responses to a variety of stresses. This stress response comes at the expense of scavenging for scarce resources, causing a trade-off between stress tolerance and nutrient acquisition. This trade-off favors non-functional rpoS alleles in nutrient-poor environments. We used experimental evolution to explore how natural selection modifies the regulatory network of strains lacking RpoS when they are evolved in an osmotically stressful environment. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7672

24 Samples

Download data: PAIR