GEO DataSets

(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) Microarray consists of full-length PCR products from all 4,290 annotated open reading frames (ORFs) in E. coli mg1655 (1). PCR products are printed in replicate on standard, 1” X 3”, poly-l-lysine coated glass microscope slides. Greater than 95% have been shown to migrate as a single band, of the predicted molecular weight, as determined by gel electrophoresis and ethidium bromide staining. Also printed on each microarray are >200 control spots consisting of: fragmented E. more...

Organism:

Escherichia coli

1 Series

5 Samples

Download data: TXT

(Submitter supplied) Expression in biofilm cells of mutants yceP and yliH relative to biofilm cells of E. coli K-12 wild type strain Keywords: comparison of strain expression profiles

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

4 Samples

Download data

(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) 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) We investigated the effect of a temperature shift from 23˚C to 37˚C, mimicking the temperature transition experienced by a microbe as it enters a human host. This strategy allowed the exploration of the kinetics of gene expression changes in immediate response to a temperature upshift and to characterize the suite of genes required to respond to 37˚C in the first few hours. We demonstrate that a significant number of genes are rapidly altered in expression within minutes to hours after a temperature shift. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL6540

9 Samples

Download data: GPR, XLSX

(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) 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) Gene expression changes between outside and inside of biofilms were investigated. The gene expression was compared between the outside and inside of the biofilms. At the same time, the gene expressions were also compared with exponential phase and stationary phase in planktonic cells. The gene expression analysis showed that the physiological activities were higher at the outside of the biofilms than those at the inside of the biofilms. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL, DCP

(Submitter supplied) The alternative sigma factor RpoS regulates transcription of many genes in Escherichia coli in response to many different stresses. The rate of change of RpoS levels in response to stress, and the consequences of that change for the temporal patterns of expression of RpoS-regulated genes has not been described. We measured the temporal pattern of RpoS levels in response to the entry to stationary phase, high osmolarity, or low temperature. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

192 Samples

Download data: TXT

(Submitter supplied) Temporal expression of biofilm and suspenion samples from E. coli wild type cultured on glass wool in LB medium. Samples removed after 4, 7, 15, and 24 hr of culturing Keywords: time course (temporal exression)

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Dataset:

GDS2768

Platform:

GPL199

8 Samples

Download data

Analysis of Escherichia coli K-12 biofilms up to 24 hours of culturing. Biofilm bacteria predominate in nutrient-sufficient ecosystems. Results provide insight into the molecular mechanisms underlying biofilm development.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array, count, 2 cell type, 4 time sets

Platform:

GPL199

Series:

GSE3905

8 Samples

Download data

(Submitter supplied) Temperature is a crucial environmental signal that govers the occurrence of Vibrio cholerae and cholera outbreaks. To understand how temperature impacts the transcriptome of V. cholerae we performed whole-genome level transcriptional profiling using custom microarrays on cells grown at human body temperature (37 C) then shifted to temperatures V. cholerae experience in the environment (15 C and 25 C).

Organism:

Vibrio cholerae

Type:

Expression profiling by array

Platform:

GPL20916

18 Samples

Download data: GPR

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

Type:

Expression profiling by array

Platform:

GPL7672

24 Samples

Download data: PAIR

(Submitter supplied) The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

4 Samples

Download data: CEL, CHP

(Submitter supplied) The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

4 Samples

Download data: CEL, CHP

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

Organism:

Pseudomonas protegens; Pseudomonas protegens Pf-5

Type:

Expression profiling by array

Platforms:

GPL7620 GPL7621

18 Samples

Download data: MEV, TXT