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Links from GEO DataSets

Items: 11

1.

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
2.

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 str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai; Escherichia coli CFT073; Escherichia coli O157:H7 str. EDL933; Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Type:
Expression profiling by array
Platforms:
GPL24239 GPL13359
19 Samples
Download data: TXT
Series
Accession:
GSE106630
ID:
200106630
3.

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 O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by array
Platform:
GPL13359
11 Samples
Download data: TXT, XLSX
Series
Accession:
GSE106628
ID:
200106628
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:
Escherichia coli K-12; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica serovar Typhimurium
Type:
Genome binding/occupancy profiling by array
Platforms:
GPL10008 GPL17580
21 Samples
Download data: TXT
Series
Accession:
GSE49914
ID:
200049914
5.

Dipyridyl Treatment

(Submitter supplied) Culture was split into halves and 500 uM dipyridyl was added to one half. Samples were collected after the indicated times. Groups of assays that are related as part of a time series. Keywords: time_series_design
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium
Type:
Expression profiling by array
Platform:
GPL3048
6 Samples
Download data
Series
Accession:
GSE3734
ID:
200003734
6.

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
7.

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
8.

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
9.

Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

(Submitter supplied) Background The osmotic regulator OmpR in Escherichia coli regulates differentially the expression of major porin proteins OmpF and OmpC. In Yersinia enterocolitica and Y. pseudotuberculosis, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in Y. pestis are not yet fully understood. Results Y. pestis OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. more...
Organism:
Yersinia pestis
Type:
Expression profiling by array
Platform:
GPL11443
4 Samples
Download data: TXT
Series
Accession:
GSE26601
ID:
200026601
10.

Expression data from Burkholderia multivorans mucoid and nonmucoid isolates

(Submitter supplied) Burkholderia multivorans comprises opportunistic bacteria infecting hosts such as cystic fibrosis (CF) patients. Bcc long-term infection of CF patient airways has been associated with emergence of phenotypic variation including the mucoid-to-nonmucoid colony morphotype. Here we studied three Burkholderia multivorans clonal isolates (mucoid D2095 (BM11L), and nonmucoid D2214G and D2214P) and a laboratory nonmucoid variant (BM11L-nmv1) obtained under prolonged stationary phase. more...
Organism:
Burkholderia multivorans; Burkholderia multivorans ATCC 17616; Burkholderia cenocepacia J2315
Type:
Expression profiling by array
Platform:
GPL13356
12 Samples
Download data: CEL
Series
Accession:
GSE111467
ID:
200111467
11.

Characterisation of modular response of E. coli Keio collection mutant library to acid adaptation

(Submitter supplied) To study the dynamics of acid adaptation in E.coli Keio collection mutant library at pH7 and pH5.5 after 15 minutes of adaptation Keywords: Single channel hybridisation were carried out using cy5 dye.
Organism:
Escherichia coli str. K-12 substr. MG1655; Escherichia coli; Escherichia coli K-12
Type:
Expression profiling by array
Platform:
GPL7535
62 Samples
Download data: CSV
Series
Accession:
GSE13361
ID:
200013361
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