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ChIP-seq of Escherichia coli RpoS during stationary phase

ABSTRACT: ChIP-seq of Escherichia coli RpoS during stationary phase

PROVIDER: PRJEB18602 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1755795.fastq.gz	Fastqsanger.gz
	ERR1755796.fastq.gz	Fastqsanger.gz

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ChIP-seq of Escherichia coli RpoS during stationary phase

Project description:To determine sites where RpoS binds (and hence likely plays a direct role in transcription), we used ChIP-seq to map the association of RpoS across the Escherichia coli chromosome during stationary phase growth in minimal medium. To facilitate ChIP, RpoS was C-terminally SPA-tagged at its native locus.

2016-12-23 | E-MTAB-5339 | biostudies-arrayexpress

Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

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BW25113 H202 and delta rpoS persister cells vs. stationary phase BW25113 wild-type

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Expression profiling of E. coli rpoS knock-out strain during stationary phase in M9 minimal media with 0.2% glucose

Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide. Data for wild type controls are GSM389302, GSM389303, and GSM389304.

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Microarray analysis of gene expression in wt, rpoS and hapR mutants in stationary phase

Project description:For expression analysis of wild-type V. cholerae, hapR, and rpoS deletion mutants in mid-exponential or stationary phase, the strains were grown to either OD600 of 0.3 or for 11 h in LB media at 37 0C, and bacteria from 2-ml culture were quickly pelleted, resuspended in Trizol reagent (GIBCO/BRL, San Diego, California, United States), and frozen on dry ice. RNA was isolated from the Trizol agent, treated with DNaseI (Ambion, Austin, Texas, United States), and cleaned by using the RNeasy kit (Qiagen, Valencia, California, United States). Labeling of cDNA and microarray hybridizations were performed as described [Yiliz et al. 2001, Mol. Micro. 53: 497-515]. Microarrays were scanned with a GenePix 400A instrument (Axon Instruments), using the GENEPIX 5.0 software. At least four microarray experiments were performed for each of two biological replicates for the tested strains. Gene expression of V. cholerae, rpoS, and hapR deletion mutants in stationary phase LB cultures was analyzed and compared to the wild-type parent under identical conditions. Gene expression of the wild-type parent during stationary phase after 11 h growth in LB was analyzed using RNA from an exponentially growing culture as a reference. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Xbp1 binding during log phase and stationary phase.

Project description:To determine where Xbp1 binds to chromatin during log phase and stationary phase, we performed ChIP-seq.

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Gene expression of E. coli MG1655 wild type and rpoS knock-out strains

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