GEO DataSets

(Submitter supplied) Cellular metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. Methods to detect these regulatory interactions are mostly based on in vitro binding assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that are potential effectors of transcription factors in E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26155

56 Samples

Download data: CSV

(Submitter supplied) ChIPexo experiment was performed on E. coli K12 MG1655 with various supplements designed to activate transcriptional regulators

Organism:

Escherichia coli K-12

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24377

4 Samples

Download data: GFF

(Submitter supplied) RNA sequencing was performed on multiple E. coli strains grown on glucose minimal media

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16085

14 Samples

Download data: CSV

(Submitter supplied) RNA sequencing was performed on E. coli K12 MG1655 with various supplements designed to activate transcriptional regulators

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

30 Samples

Download data: CSV

(Submitter supplied) Previously unpublished expression data from E. coli K-12 MG1655 involved in the creation of a large RNAseq database.

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli BW25113

Type:

Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: CSV

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL25406

9 Samples

Download data: PAIR

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL25406

35 Samples

Download data: PAIR

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

Organism:

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

Type:

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

Platforms:

GPL17439 GPL16085

16 Samples

Download data: GFF

(Submitter supplied) The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16085

8 Samples

Download data: CSV

(Submitter supplied) The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17439

8 Samples

Download data: GFF

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL15010

50 Samples

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(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL15010

20 Samples

Download data: CSV

(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability during exponential growth in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15010

20 Samples

Download data: CSV

(Submitter supplied) Analysis of RNA binding partners of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL15010

10 Samples

Download data: CSV

(Submitter supplied) The experiment is a time course for the aerobic to anaerobic switch response in E. coli. The data was used to validate the utility of a set of predicted transcription factor gene interactions for modeling the dynamic regulatory response networks of this response. The transcription factor gene interaction predictions were generated by a semi-supervised classification method that takes advantage of a separate compendium of gene expression and a data set of curated interactions. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platforms:

GPL5435 GPL5436

11 Samples

Download data: XLS

(Submitter supplied) This study examined the genes under the control of FlhDC and sigmaF in E. coli. Keywords: wild-type, deletion and overexepression strains

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

15 Samples

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(Submitter supplied) Our laboratory has recently discovered that E. coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for Thymineless Death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses on actively growing optA1 gpt strains subjected to hypoxanthine deprivation for increasing periods of time. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL3154

90 Samples

Download data: CEL, CHP

(Submitter supplied) In a given bacterial population, antibiotic treatment kills a large portion of the population, while a small, tolerant subpopulation survives. Tolerant cells disrupt the efficacy of antibiotic treatment and increase the likelihood that a population gains antibiotic resistance. Antibiotic tolerance is different from resistance because tolerant cells cannot grow and replicate in the presence of the antibiotic, but when the antibiotic is removed, they begin to propagate. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

18 Samples

Download data: CSV

(Submitter supplied) Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL

(Submitter supplied) E.coli K-12 W3110 was grown in LB medium and harvested at each time point. And time series microarray experiments were performed based on reference desgin. In reference design, the control sample is collected at one representative time point. Combining with data from sequential design, more acculate and reliable expression series could be collected. Keywords: Reference design

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL4374

22 Samples

Download data: TXT