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

ABSTRACT: 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.

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

PROVIDER: GSE26054 | GEO | 2011/12/01

SECONDARY ACCESSION(S): PRJNA135559

REPOSITORIES: GEO

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

2011-06-14 | GSE26589 | GEO

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

Escherichia coli str. K-12 substr. MG1655

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

| PRJNA135559 | ENA

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

2014-02-05 | GSE46541 | GEO

Arginine-dependent gene regulation in Streptococcus gordonii ArgR regulator knockout

Project description:We have previously shown that responses of the oral bacterium Streptococcus gordonii to arginine are co-ordinated by three paralogous regulators: ArgR, ArgR and AhrC. This set of experiments was designed to assess the effects of the ArgR gene regulator on global gene expression in Streptococcus gordonii under high arginine or following a shift to no arginine.

2017-07-18 | GSE101506 | GEO

ArcA Chip-chip from Escherichia coli MG1655 K-12, WT and ∆arcA strains

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

2013-10-17 | GSE46413 | GEO

High throughput analysis of binding of E. coli Lrp mutants

Project description:Feast-Famine Response Proteins are a widely conserved class of global regulators in prokaryotes, the most highly studied of which is the E. coli leucine-responsive regulatory protein (Lrp). Lrp senses environmental nutrition status and subsequently regulates up to one-third of the genes in E. coli, either directly or indirectly. Lrp exists predominantly as octamers and hexadecamers (16mers), where leucine is believed to shift the equilibrium towards the octameric state. In this study, we analyzed the effects of three oligomerization state mutants of Lrp in terms of their ability to bind to DNA and regulate gene expression in response to exogenous leucine. We find that oligomerization beyond dimers is required for Lrp’s regulatory activity, and that contrary to prior speculation, exogenous leucine modulates Lrp activity at its target promoters exclusively by inhibiting Lrp binding to DNA. We also find evidence that Lrp binding bridges DNA over length scales of multiple kilobases, revealing a new range of mechanisms for Lrp-mediated transcriptional regulation.

2023-01-31 | GSE198120 | GEO

Chip-chip from Escherichia coli MG1655 K-12, WT and ∆fnr strains

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

2013-06-20 | GSE41186 | GEO

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

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