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.
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.
Project description:Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The ∆hns/∆stpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
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