Similar studies for GEO DataSets (Select 200066481) - GEO DataSets

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Items: 20

Select item 2000664811.

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]

(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

Series

Accession:: GSE66481

ID:: 200066481

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Select item 2000664822.

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli

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

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

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

Platforms:: GPL17439 GPL16085
16 Samples

Download data: GFF

Series

Accession:: GSE66482

ID:: 200066482

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Select item 2000664413.

Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [ChIP-seq]

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17439
8 Samples

Download data: GFF

Series

Accession:: GSE66441

ID:: 200066441

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Select item 2000671194.

Polyamines induce the glutamate decarboxylase acid response system by increasing the level of the σ38 subunit (RpoS) of Escherichia coli RNA polymerase via gadE regulon

(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

Series

Accession:: GSE67119

ID:: 200067119

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Select item 2000499185.

Polyamines are critical for the induction of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli

(Submitter supplied) As part of our studies on the biological functions of polyamines we have used a mutant of Escherichia coli that lacks all the genes for polyamine biosynthesis for a global transcription analysis on the effect of added polyamines. The most striking early response to polyamine addition is the increased expression of the genes for the glutamate dependent acid resistance system (GDAR) that is essential for the survival of bacteria when passing through the acid environment of the stomach. more...

Organism:: Escherichia coli

Type:: Expression profiling by array

Platform:: GPL3154
12 Samples

Download data: CEL, CHP

Series

Accession:: GSE49918

ID:: 200049918

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Select item 2000657126.

Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress

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

Organism:: Escherichia coli

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

Platform:: GPL16085
14 Samples

Download data: GFF

Series

Accession:: GSE65712

ID:: 200065712

PubMed Similar studies

Select item 2000657117.

Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]

(Submitter supplied) Oxidative stress that originates from reactive oxygen species (ROS) is an inevitable consequence of aerobic respiration in bacteria. Three transcription factors (TFs), OxyR, SoxR, and SoxS play a critical role in transcriptional regulation of the defense system. However, the full genome-wide regulatory potential of them remains elusive. Here, we comprehensively reconstruct genome-wide OxyR, SoxR, and SoxS transcriptional regulatory networks in Escherichia coli under oxidative stress. more...

Organism:: Escherichia coli

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16085
8 Samples

Download data: CSV

Series

Accession:: GSE65711

ID:: 200065711

PubMed Similar studies SRA Run Selector

Select item 2000657108.

Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [ChIP-seq]

Organism:: Escherichia coli

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL16085
6 Samples

Download data: GFF

Series

Accession:: GSE65710

ID:: 200065710

PubMed Similar studies SRA Run Selector

Select item 2000889819.

Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655

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

Organism:: Escherichia coli str. K-12 substr. MG1655

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

Platform:: GPL17439
6 Samples

Download data: GFF

Series

Accession:: GSE88981

ID:: 200088981

PubMed Full text in PMC Similar studies

Select item 20008898010.

Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]

(Submitter supplied) A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. more...

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17439
4 Samples

Download data: CSV

Series

Accession:: GSE88980

ID:: 200088980

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Select item 20008897911.

Organism:: Escherichia coli str. K-12 substr. MG1655

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL17439
2 Samples

Download data: GFF

Series

Accession:: GSE88979

ID:: 200088979

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Select item 20016579412.

Time series (T= 0-4 hours) for E. coli K-12 MC4100 after a shift from 23˚C to 37˚C (M9 minimal glycerol medium, exponential phase growth)

(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

Series

Accession:: GSE165794

ID:: 200165794

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Select item 20005768913.

Analysis of the evolutionary adaptation of an AraC-like global regulatory protein in the murine enteric pathogen Citrobacter rodentium

(Submitter supplied) An experiment to test the equivalence of the Citrobacter rodentium RegA and E.Coli SMS 3-5 homologue

Organism:: Citrobacter rodentium

Type:: Expression profiling by array

Platform:: GPL7345
16 Samples

Download data: TXT

Series

Accession:: GSE57689

ID:: 200057689

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Select item 20008785614.

The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.

(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

Series

Accession:: GSE87856

ID:: 200087856

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Select item 20013199215.

Systematic identification of metabolites controlling gene expression in E. coli

(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

Series

Accession:: GSE131992

ID:: 200131992

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Select item 20000832316.

Dynamics of Ecoli Aerobic to Anaerobic Switch Response

(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

Series

Accession:: GSE8323

ID:: 200008323

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Select item 20015689617.

Regulatory proteins control a transcriptional network in response to antibiotic stress

(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...