Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-chip of MG1655 with antibody against E. coli RNAP beta subunit under various conditions

ABSTRACT: We integrated RNAP binding regions (RBRs) and mRNA transcript abundance to determine segments of contiguous transcription originating from promoter regions. To measure RBRs at a genome scale, we employed a ChIP-chip method to E. coli K-12 MG1655 grown in the presence or absence of rifampicin under multiple growth conditions using antibody against E. coli RNAP beta subunit. A twelve ChIP-chip study using immunoprecipitated DNA (IP-DNA) from four separate culture conditions with and/or without rifampicin treatment. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome (NimbleGen). Experiments were conducted as biological duplicates or triplicates (different cultures).

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Bernhard Palsson

PROVIDER: E-GEOD-15588 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The transcription unit architecture of the Escherichia coli genome.

Cho Byung-Kwan BK Zengler Karsten K Qiu Yu Y Park Young Seoub YS Knight Eric M EM Barrett Christian L CL Gao Yuan Y Palsson Bernhard Ø BØ

Nature biotechnology 20091101 11

Bacterial genomes are organized by structural and functional elements, including promoters, transcription start and termination sites, open reading frames, regulatory noncoding regions, untranslated regions and transcription units. Here, we iteratively integrate high-throughput, genome-wide measurements of RNA polymerase binding locations and mRNA transcript abundance, 5' sequences and translation into proteins to determine the organizational structure of the Escherichia coli K-12 MG1655 genome. ...[more]

PMID: 19881496

Similar Datasets

ChIP-chip of E. coli K-12 MG1655 with antibody against RNA polymerase subunits, RpoB, RpoD, RpoS,RpoH, RpoN, FliA, and FecI

Project description:We investigate sigma factor binding regions for each sigma factor under various enviromental and/or genetic conditions. To measure sigma factor binding at a genome scale, we employed a ChIP-chip method to derivative strains of E. coli K-12 MG1655 wild type and its isogenic rpoS and rpoN knock-out strains under various conditions. A 45 ChIP-chip study under 4 separate culture conditions. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome.

2014-02-05 | E-GEOD-46541 | biostudies-arrayexpress

Transcriptome analysis of E.coli MG1655 under multiple growth conditions

Project description:Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and nitrogen-limiting condition. A fourteen chip study using total RNA recovered from four separate culture conditions of E.coli K12 MG1655. E.coli strains were harvested at mid-exponential phase with exception of stationary phase experiments. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome (NimbleGen). Experiments were conducted as three or more biological replicates (different cultures)

2009-11-03 | E-GEOD-15534 | biostudies-arrayexpress

RNA polymerase

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-02-05 | E-GEOD-46740 | biostudies-arrayexpress

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

Project description:This SuperSeries is composed of the following subset Series: GSE26588: Transcriptome analysis of E. coli MG1655 GSE26589: ChIP-chip of E. coli K-12 MG1655 with antibody against PurR-8myc under various conditions. Refer to individual Series

2012-01-12 | E-GEOD-26591 | biostudies-arrayexpress

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

Project description: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. A four ChIP-chip study under two separate culture conditions. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome.

2011-06-14 | E-GEOD-26589 | biostudies-arrayexpress

ChIP-chip of E. coli K-12 MG1655 with antibody against ArgR-8myc, Lrp-8myc, and TrpR-8myc under various conditions.

Project description:We integrated transcription factor binding regions and mRNA transcript abundance to elucidate the ArgR, Lrp, and TrpR 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 ArgR-8myc, Lrp-8myc, or TrpR-8myc under various conditions. A twelve ChIP-chip study under six separate culture conditions. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome.

2011-12-01 | E-GEOD-26054 | biostudies-arrayexpress

ChIP-seq of E. coli to identify H-NS and Fis binding at multiple time-points during growth in rich medium

Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear.<br><br>Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.

2010-09-01 | E-MTAB-332 | biostudies-arrayexpress

Determining the control circuitry of redox metabolism at the genome-scale

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-02-27 | E-GEOD-55367 | biostudies-arrayexpress

ChIP-chip of Geobacter sulfurreducens PCA with antibody against RNAP and RpoD under various conditions

Project description:We applied a ChIP-chip approach to elucidate the binding profiles of RNAP and RpoD experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays. A 21 ChIP-chip study using immunoprecipitated DNA (IP-DNA) from three culture conditions for RNAP and four culture conditions for RpoD. The high-density oligonucleotide tiling arrays used consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G. sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures).

2010-07-01 | E-GEOD-22503 | biostudies-arrayexpress

ChIP-chip of Geobacter sulfurreducens PCA with antibody against RpoN under various conditions.

Project description:We applied a ChIP-chip approach to elucidate the σN regulon experimentally under different growth conditions. This technique localizes DNA fragments within σN complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays. A nine ChIP-chip study using immunoprecipitated DNA (IP-DNA) from three separate culture conditions. The high-density oligonucleotide tiling arrays used were consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G.sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures)

2010-06-30 | E-GEOD-17837 | 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