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

ABSTRACT: 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).

ORGANISM(S): Geobacter sulfurreducens PCA

SUBMITTER: Bernhard Palsson

PROVIDER: E-GEOD-22503 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Structural and operational complexity of the Geobacter sulfurreducens genome.

Qiu Yu Y Cho Byung-Kwan BK Park Young Seoub YS Lovley Derek D Palsson Bernhard Ø BØ Zengler Karsten K

Genome research 20100630 9

Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding informatio ...[more]

PMID: 20592237

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Analysis of Geobacter sulfurreducens under multiple growth conditions

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ChIP-chip of Geobacter sulfurreducens PCA with antibody against various sigma factors under various conditions

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

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2010-06-30 | E-GEOD-17834 | biostudies-arrayexpress

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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.

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Analysis of the iron stimulon and fur regulon of Geobacter sulfurreducens [ChIP-chip]

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