GEO DataSets

(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) Wild-type E. coli are prototrophic for all amino acid and nucleotides. These are synthesized by a network of interconnected metabolic pathways from a handful precursors molecules, which are regulated at the level of gene expression. It was hypothesized in this study, that since metabolic pathways are interconnected, transcriptional regulation should be shared across multiple pathways. To uncover these regulatory interactions, cells growing at steady state were perturbed by the addition of an end-metabolite (aa or nt), and were allowed to recover. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL3503

22 Samples

Download data: GPR

(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) 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) 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) Analysis of effect of deletion of the two transcriptional factors KdpE and Cra on gene expression of EHEC 8624

Organism:

Escherichia coli; Escherichia coli 8624

Type:

Expression profiling by array

Platform:

GPL3154

3 Samples

Download data: CEL, CHP

(Submitter supplied) We measured the response of S. cerevisiae to arrest in the presence of alpha factor. These were collected in support of a related DNaseI-sequencing study. Keywords: Alpha-factor arrest

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

2 Samples

Download data: CEL, CHP