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Title: Genome-wide characterization of PhoB binding profile in Escherichia coli (ChIP-chip data)      
dateReleased:
10-21-2012
description:
Chromatin immunoprecipitation was combined with high-density tiling array (ChIP-chip) and gene expression microarray to reveal the adaptive responses of Escherichia coli to phosphate starvation. The first sketch of the genome-wide distribution of PhoB binding profile was unveiled and 43 regions were identified as the PhoB binding regions. The presence of a significant common motif in these binding regions allowed us to reconstruct the PhoB binding pattern. By comparing the ChIP-chip and microarray datasets, we were also able to identify genes directly or indirectly affected through PhoB regulation. Nineteen out of the 287 differentially expressed genes in the presence and absence of PhoB activity were considered as the genes directly regulated by PhoB. The adaptive responses affected through PhoB regulation are discussed and these responses involve in several important biological functions including transcriptional regulation, transportation, membrane component arrangement, sigma factor modulation and DNA replication inhibition. Comparison of the E. coli K12 MG1655 wild type and a PhoB-FLAG fusion expressing strain (MG1655_PhoB_FLAG). The anti-FLAG antibody was used to recognize PhoB-FLAG fusion protein. Therefore, ChIPed DNA from the wild type strain was used as the control group. Three biological replicates were performed.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-21856
refinement:
raw
alternateIdentifiers:
21856
keywords:
functional genomics
dateModified:
05-02-2014
availability:
available
types:
gene expression
name:
Escherichia coli
ID:
A-GEOD-10416
name:
NimbleGen E. coli K12 Mg1655 385K array
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21856/E-GEOD-21856.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21856/E-GEOD-21856.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21856
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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