Transcriptomics

Dataset Information

61

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


ABSTRACT: 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.

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

SUBMITTER: Bernhard O Palsson   Donghyuk Kim  Byung-Kwan Cho 

PROVIDER: E-GEOD-46541 | ArrayExpress | 2014-02-05

SECONDARY ACCESSION(S): GSE46541PRJNA202223

REPOSITORIES: GEO, ArrayExpress

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Publications

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.

Cho Byung-Kwan BK   Kim Donghyuk D   Knight Eric M EM   Zengler Karsten K   Palsson Bernhard O BO  

BMC biology 20140124


At the beginning of the transcription process, the RNA polymerase (RNAP) core enzyme requires a σ-factor to recognize the genomic location at which the process initiates. Although the crucial role of σ-factors has long been appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function.Using multiple genome-scale measurements, we elucidated the network of σ-factor and promoter interactions in Escherichia coli. The reconstructed network  ...[more]

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