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Links from GEO DataSets

Items: 20

1.

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 [ChIP-exo]

(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:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17439
2 Samples
Download data: GFF
Series
Accession:
GSE88979
ID:
200088979

PubMed Full text in PMC Similar studies SRA Run Selector

2.

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

3.

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

PubMed Full text in PMC Similar studies SRA Run Selector

4.

ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 μg/ml)

(Submitter supplied) OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently, OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium; Escherichia coli K-12; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Type:
Genome binding/occupancy profiling by array
Platforms:
GPL10008 GPL17580
21 Samples
Download data: TXT
Series
Accession:
GSE49914
ID:
200049914

PubMed Full text in PMC Similar studies Analyze with GEO2R

5.

Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

(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
20 Samples
Download data: GFF
Series
Accession:
GSE54901
ID:
200054901

PubMed Full text in PMC Similar studies

6.

Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]

(Submitter supplied) The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). more...
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17439
8 Samples
Download data: CSV
Series
Accession:
GSE54900
ID:
200054900

PubMed Full text in PMC Similar studies SRA Run Selector

7.

Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [ChIP-Seq]

(Submitter supplied) The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism in many bacteria. However, the full regulatory potential of Fur beyond iron metabolism remains undefined. Here, we comprehensively reconstructed the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). more...
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17439
12 Samples
Download data: GFF
Series
Accession:
GSE54899
ID:
200054899

PubMed Full text in PMC Similar studies SRA Run Selector

8.

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

9.

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

10.

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

11.

Genome-scale reconstruction of the PurR regulon reveals its role in the adenine stimulon of Escherichia coli K-12 MG1655

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli str. K-12 substr. MG1655; Escherichia coli
Type:
Expression profiling by array; Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL3154 GPL8387
12 Samples
Download data: CEL, PAIR
Series
Accession:
GSE26591
ID:
200026591

PubMed Full text in PMC Similar studies Analyze with GEO2R

12.

ChIP-chip of E. coli K-12 MG1655 with antibody against PurR-8myc under various conditions.

(Submitter supplied) We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the PurR regulon experimentally. To measure transcription factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 harboring PurR-8myc under various conditions.
Organism:
Escherichia coli str. K-12 substr. MG1655
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL8387
4 Samples
Download data: PAIR
Series
Accession:
GSE26589
ID:
200026589

PubMed Full text in PMC Similar studies Analyze with GEO2R

13.

Transcriptome analysis of E. coli MG1655

(Submitter supplied) Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine.
Organism:
Escherichia coli; Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by array
Platform:
GPL3154
8 Samples
Download data: CEL
Series
Accession:
GSE26588
ID:
200026588

PubMed Full text in PMC Similar studies Analyze with GEO2R

14.

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; 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
Series
Accession:
GSE66482
ID:
200066482

PubMed Full text in PMC Similar studies

15.

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

PubMed Full text in PMC Similar studies SRA Run Selector

16.

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

PubMed Full text in PMC Similar studies SRA Run Selector

17.

E.coli GeneChip study of E.coli responses to osmotic and heat stresses

(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
Series
Accession:
GSE7656
ID:
200007656

PubMed Full text in PMC Similar studies Analyze with GEO2R

18.

To compare the transcriptome of ompR null strains with wild-type strain of E. coli and S. Typhimurium during stress

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Escherichia coli O157:H7 str. EDL933; Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S; Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platforms:
GPL24239 GPL13359
19 Samples
Download data: TXT
Series
Accession:
GSE106630
ID:
200106630

PubMed Full text in PMC Similar studies Analyze with GEO2R

19.

To compare the transcriptome of ompR null strains with wild-type strain of S. Typhimurium during osmotic stress

(Submitter supplied) In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in S. Typhimurium responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Type:
Expression profiling by array
Platform:
GPL24239
8 Samples
Download data: TXT, XLSX
Series
Accession:
GSE106629
ID:
200106629

PubMed Full text in PMC Similar studies Analyze with GEO2R

20.

To compare the transcriptome of ompR null strains with wild-type strain of E. coli during acid or osmotic stress

(Submitter supplied) In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in E. coli responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. more...
Organism:
Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai
Type:
Expression profiling by array
Platform:
GPL13359
11 Samples
Download data: TXT, XLSX
Series
Accession:
GSE106628
ID:
200106628

PubMed Full text in PMC Similar studies Analyze with GEO2R

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