GEO DataSets

Expression profiling of cells at various time points up to 10 minutes following induction by IPTG of alternative sigma factor, sigma32, from an inducible promoter. Sigma32 mediates the heat shock response. Results identify genes regulated by sigma32.

Organism:

Escherichia coli

Type:

Expression profiling by array, log2 ratio, 2 agent, 5 time sets

Platform:

GPL3500

Series:

GSE4321

16 Samples

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(Submitter supplied) DNA microarray analysis of genes regulated by the alternative sigma factor, sigma 32 (rpoH). Sigma 32-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma 32, with a strain over-expressing sigma 32 (following induction of rpoH from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses. Because sigma 32 is negatively regulated, its activity decreases 10 min after overexpression. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Dataset:

GDS1804

Platform:

GPL3500

16 Samples

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(Submitter supplied) This study examined the genes under the control of sigma32 in E. coli by moderate induction of a plasmid-borne rpoH gene under defined steady-state growth condition. Samples were taken from culture at mid log phase (OD=0.2) before or 5 minutes, 10 minutes or 15 minutes after induction. Samples were then RNA-stabilized using Qiagen RNAProtect Bacterial Reagent (Qiagen). Total RNA was then isolated using MasterPure kits (Epicentre Technologies). more...

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL199

8 Samples

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(Submitter supplied) Vibrio cholerae, the cause of cholera, can grow in a variety of environments outside of human hosts. During infection, the pathogen must adapt to significant environmental alterations, including the elevated temperature of the human gastrointestinal tract. σ32, an alternative sigma factor encoded by rpoH, activates transcription of genes involved in the heat-shock response in several bacterial species. more...

Organism:

Vibrio cholerae; Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by array

Platform:

GPL3651

6 Samples

Download data: TXT

(Submitter supplied) cDNA microarray analysis to identify genes regulated by the RNA chaperone, Hfq. Four experiments were performed: 1/ Hfq+ vs Hfq- strains. 269 significantly differentially regulated genes were identified by SAM (Statistical Analysis of Microarrays), of which 120 changed more than 1.5 fold (48 increased and 72 decreased in hfq-). Amongst other genes, these experiments identified significant regulation of the sigma E and sigma 32 regulons. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platforms:

GPL3500 GPL4620 GPL2928

21 Samples

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(Submitter supplied) DNA microarray analysis of genes regulated by the alternative sigma factor, sigma E (rpoE). Sigma E-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma E, with a strain over-expressing sigma E (following induction of rpoE from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses after induction and used SAM (Statistical Analysis of Microarrays) to identify 75 significantly induced and 8 significantly repressed genes. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platforms:

GPL2928 GPL2926 GPL2927

21 Samples

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

Organism:

Cereibacter sphaeroides 2.4.1

Type:

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

Platforms:

GPL162 GPL10463

21 Samples

Download data: CEL, PAIR

(Submitter supplied) In this study, we performed expression profiling experiments to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and compared the global gene expression profiles.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL162

15 Samples

Download data: CEL

(Submitter supplied) In this study, we performed a ChIP-chip experiment to determine the respective regulons of RpoHI and RpoHII in Rhodobacter sphaeroides. We grew R. sphaeroides in aerobic conditions and induced either proteins ectopically and immuno-precipitated the regions of the genomic DNA interacting with the sigma factors.

Organism:

Cereibacter sphaeroides 2.4.1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10463

6 Samples

Download data: PAIR

(Submitter supplied) We probed the mechanism of cross-regulation of osmotic and heat stress responses by characterizing the effects of high osmolarity (0.3M vs. 0.0M NaCl) and temperature (43oC vs. 30oC) on the transcriptome of Escherichia coli K12 using E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures). Total RNA was extracted using a hot phenol-chloroform method. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

18 Samples

Download data: CEL, CHP

(Submitter supplied) The ArrayIt® brand SuperAmine 2 Microarray Substrates line represents the highest quality amine-containing substrate in the microarray industry. All of our substrates are polished to atomic flatness and manufactured in a state-of-the-art class 100 cleanrooms, with strict controls on particulate, biological and static contaminants, as well as temperature and humidity control.  These pristine glass substrates with reactive amine groups offer quality and performance that cannot be obtained from any other vendor. more...

Organism:

Shewanella oneidensis MR-1

9 Series

166 Samples

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(Submitter supplied) Recombinant Escherichia coli cultures are used to manufacture numerous therapeutic proteins and industrial enzymes, where many of these processes use elevated temperatures to induce recombinant protein production. The heat-shock response in wild-type E. coli has been well studied. In this study, the transcriptome profiles of recombinant E. coli subjected to a heat-shock and to a dual heat-shock recombinant protein induction were examined. more...

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL199

18 Samples

Download data: CEL

(Submitter supplied) The heat shock response is critical for organisms to survive at a high temperature. Heterologous expression of eukaryotic molecular chaperons protects Escherichia coli against heat stress. Here we report that expression of the plant E3 ligase BnTR1 significantly increase the thermotolerance of Escherichia coli. Different from eukaryotic chaperones, BnTR1 post-transcriptionally regulates the heat shock factor σ32 though zinc fingers of the RING domain, which interacts with DnaK resulting in stabilizing σ32 and subsequently up-regulating heat shock proteins. more...

Organism:

Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL13360

12 Samples

Download data: TXT

(Submitter supplied) Proteotoxic stress such as heat shock causes heat-shock factor (HSF)-dependent transcriptional upregulation of chaperones. Heat shock also leads to a rapid and reversible downregulation of many genes, a process we term stress-induced transcriptional attenuation (SITA). The mechanism underlying this conserved phenomenon is unknown. Here we report that enhanced recruitment of negative transcription elongation factors to gene promoters in human cell lines induces SITA. more...

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL18573 GPL21290

50 Samples

Download data: BW, TXT

(Submitter supplied) Genetically programmed deaths play important roles in the biology of unicellular prokaryotic cells. Some gene complexes force their maintenance on the host bacterial cells by killing cells that have lost them. This form of programmed death called post-segregational killing or genetic addiction is brought about by several Type II restriction-modification gene complexes, through restriction attack on the undermethylated chromosome, and underlie their behavior as selfish mobile elements. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

24 Samples

Download data: CEL

(Submitter supplied) A genome reduced E. coli strain MDS42 and its parent strain MG1655 were applied for the comparative transcriptome analysis. Genome-wide transcriptional changes due to genome reduction and heat shock were comprehensively evaluated.

Organism:

Escherichia coli

Type:

Expression profiling by genome tiling array

Platform:

GPL13336

20 Samples

Download data: CEL, TXT

(Submitter supplied) RNAseq analysis was performed on 90 E. coli samples in order to identify the transcriptional cellular response to the burden of heterologous gene expression Early responsive promoters that are upregulated in response to burden were identified. The htpG1 early responsive promoter was selected to guide the activation of a burden- responsive feedback controller able to decrease heterologous gene expression while rescuing cellular capacity and growth

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

90 Samples

Download data: CSV