Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome wide binding sites of NsrR in uropathogenic E.coli CFT073

ABSTRACT: We applied ChIP-seq to identify genome wide binding targets of NsrR in E.coli CFT073. NsrR is a nitric oxide sensitive regulator of transcription. Genome wide binding targets of NsrR have been identified in E.coli K12 using ChIP-chip. The genome of CFT073 is about 0.6Mb larger than that of K12. In this study, we identify the novel NsrR binding sites in CFT073. The nsrR gene was modified by the addition of DNA sequences encoding a C-terminal 3X-Flag tag, and the tagged gene was integrated into the chromosome. NsrR bound DNA was isolated by chromatin immunoprecipitation and it was sequenced using Miseq platform.

ORGANISM(S): Escherichia coli CFT073

SUBMITTER: Stephen Spiro

PROVIDER: E-GEOD-69829 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome wide binding sites of NsrR in uropathogenic E.coli CFT073

Project description:We applied ChIP-seq to identify genome wide binding targets of NsrR in E.coli CFT073. NsrR is a nitric oxide sensitive regulator of transcription. Genome wide binding targets of NsrR have been identified in E.coli K12 using ChIP-chip. The genome of CFT073 is about 0.6Mb larger than that of K12. In this study, we identify the novel NsrR binding sites in CFT073.

2015-06-15 | GSE69829 | GEO

Localization of NsrR binding sites in the Escherichia coli genome

Project description:NsrR is a nitric oxide sensitive regulator of transcription. In Escherichia coli, NsrR is a repressor of the hmp gene encoding the flavohemoglobin that detoxifies nitric oxide. Several other transcription units (including ytfE, ygbA and hcp-hcr) are known to be subject to regulation by NsrR. In this study, chromatin immunoprecipitation and microarray analysis was used to identify NsrR binding sites in the chromosome of Escherichia coli strain MG1655. Keywords: ChIP-chip

2008-11-19 | GSE11230 | GEO

Inefficient translation of nsrR constrains behavior of the NsrR regulon in Escherichia coli

Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 nsrR with AUG start codon compared to the wild type nsrR (with a GUG start codon) and to the control lacking the nsrR gene. Conversion of the nsrR start codon from the wild type GUG to AUG increased the efficiency of translation and had measurable effects on the expression patterns of some NsrR regulated genes. A nine chip study using total RNA recovered from three separate cultures of Escherichia coli MG1655 K-12 AUGnsrR, three separate cultures of the WT nsrR (GUGnsrR) and three separate cultures of nsrR deletion strain. Each chip measures the expression level of 4,254 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with 2-fold technical redundancy.

2015-06-27 | E-GEOD-70325 | biostudies-arrayexpress

Escherichia coli CFT073

Project description:Genome wide binding sites of NsrR in uropathogenic E.coli CFT073

| PRJNA286884 | ENA

Inefficient translation of nsrR constrains behavior of the NsrR regulon in Escherichia coli

2015-06-27 | GSE70325 | GEO

The nsrR regulon in Salmonella Typhimurium 14028s

Project description:In this study, we have defined the NsrR regulon in Salmonella enterica sv. Typhimurium 14028s using a transcriptional microarray. Wild-type and nsrR mutant S. Typhimurium were grown aerobically to early log-phase (OD600~0.5) at 37C in LB medium. Total RNA was isolated from three independent cultures of both strains and interrogated on a PCR product array representing almost all ORFs.

2012-11-21 | GSE32585 | GEO

NsrR and ResD binding in Bacillus subtilis

Project description:The direct roles of the NO-sensitive NsrR repressor and the ResD response regulator in transcriptional control in Bacillus subtilis

2013-11-22 | E-MEXP-3882 | biostudies-arrayexpress

Expression data in wild type and NsrR-null mutant of B. subtilis

2011-10-28 | GSE33289 | GEO

The NsrR regulon of Escherichia coli K-12

Project description:Successful pathogens must be able to protect themselves against reactive nitrogen species generated either as part of host defence mechanisms, or as products of their own metabolism. The regulatory protein, NsrR (a member of the Rrf2 family of transcription factors), plays key roles in this stress response. Microarray analysis was carried out to reveal the regulon of NsrR. Keywords: Response to repressor titration and different growth conditions

2007-05-18 | GSE6781 | GEO

Expression data in wild type and NsrR-null mutant of B. subtilis

Project description:NsrR strongly represses transcription of small numbers of genes in the absence of NO NsrR moderately represses transcription of large numbers of genes in a less NO-sensitive manner The wild-type and mutant cells were cultured anaerobically in the presence and absence of NO. Biological triplicate samples were used to isolate RNA.

2011-10-27 | E-GEOD-33289 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data