Unknown,Transcriptomics,Genomics,Proteomics

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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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Publications

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]

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