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Growth-phase dependent regulation of transcription by Rsd and 6S RNA

ABSTRACT: This entry refers to transcriptome analysis of five E. coli strains: E. coli K-12 MG1655, single deletions of rsd, ssrS, and rpoS, as well as a double deletion of rsd and ssrS, in five growth phases.

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

PROVIDER: GSE74809 | GEO | 2016/06/10

SECONDARY ACCESSION(S): PRJNA301595

REPOSITORIES: GEO

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Growth-phase dependent regulation of transcription by Rsd and 6S RNA

Project description:This entry refers to transcriptome analysis of five E. coli strains: E. coli K-12 MG1655, single deletions of rsd, ssrS, and rpoS, as well as a double deletion of rsd and ssrS, in five growth phases. 25 samples (5 strains in 5 growth phases) with 2 replicates each.

2016-06-10 | E-GEOD-74809 | biostudies-arrayexpress

Rsd timecourse

Project description:The gene expression profile of MC4100 delta rsd with pACYC Rsd and pACYC delta BS plasmids has been analysed using whole genome oligonucleotide microarrays. Control RNA was isolated from 50ml LB cultures of MC4100 delta rsd strain with pACYC delta BS. Experimental RNA was isolated from 50ml LB cultures of MC4100 delta rsd with pACYC Rsd, for each growth condition (OD600 = 0.4: log phase, 0.9: late log phase, 1.1: transition phase, ST(OD600 = >2.0): stationary phase). The experiments performed replicate. Keywords: timecourse (overproduction of Rsd)

2007-10-22 | GSE5981 | GEO

Sigma38 binding sites in E. Coli

Project description:ChIP-seq to identify sigma38 binding sites in wild-type and delta ssrS (6S RNA knockout) strains of E. Coli K-12 MG1655, during stationary phase

2016-06-10 | GSE74836 | GEO

Sigma38 binding sites in E. Coli

Project description:ChIP-seq to identify sigma38 binding sites in wild-type and delta ssrS (6S RNA knockout) strains of E. Coli K-12 MG1655, during stationary phase ChIP-seq using antibody against sigma38 in wild-type and ssrS deletion strain. Two replicates for wild type and one replicate for ssrS deletion.

2016-06-10 | E-GEOD-74836 | biostudies-arrayexpress

RpoS regulation of gene expression during exponential growth of E. coli K-12

2007-12-28 | GSE9814 | GEO

Expression analysis of Caenorhabditis elegans Bristol N2 rsd-2 and rsd-6 single mutants at 25°C and 20°C

2013-06-01 | GSE40459 | GEO

Transgenerational profiling of small non-coding RNAs in C.elegans RSD mutants

Project description:Attempt to identify progressive changes in small non-coding RNA levels in C.elegans lacking RSD-2 or RSD-6.

2013-06-01 | GSE40457 | GEO

Expression analysis of Caenorhabditis elegans Bristol N2 rsd-2 and rsd-6 single mutants at 25Â°C and 20Â°C

Project description:Investigation of whole genome gene expression level changes in early generation Caenorhabditis elegans Bristol N2 rsd-2 and Bristol N2 rsd-6 single mutants, compared to late-generation strains at 25Â°C and 20Â°C A six chip study using total RNA recovered from two separate alleles of Caenorhabditis elegans Bristol N2 rsd-2 and one allele Bristol N2 rsd-6 , in which the effects of transgeneration aging are studied in early generation animals and late generation animals at the restrictive temperature of 25Â°C and the permissive temperature, 20Â°C.

2013-06-01 | E-GEOD-40459 | biostudies-arrayexpress

Transcription profiling of E.coli wild type vs RpoS mutants during exponenitail growth

Project description:This study is to identify the RpoS regulon in MG1655 in early exponential growth. RNA samples from wild type or rpoS mutants were extracted using acidic hot phenol method and hybridized to Affymetrix E. coli Antisense Genome Array. Experiment Overall Design: A precise rpoS deletion mutant of MG1655 was constructed using the red recombinase method. Wild type and rpoS mutants were inoculated in triplicate into LB media at a starting OD of 0.0001 and grown aerobically at 37C. Cultures were harvested at an OD600 = 0.3 after being maintained in exponential phase for at least eight generations. For RNA extraction, cultures were mixed directly with a boiling lysis buffer containing SDS and EDTA followed by acidic hot phenol (65C) to minimize RNA degradation. RNA samples were hybridized to Affymetrix E. coli Antisense Genome Array according to Affymetrix's standard protocols.

2008-06-16 | E-GEOD-9814 | biostudies-arrayexpress

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

Project description:The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). Genes involved in the energy metabolism and the flagella synthesis showed higher expression in the rpoS knock-out biofilms (MBF), but not in the wild type biofilms (WBF). Moreover, genes involved in the stress responses showed higher expression in the wild type biofilms (WBF), but not in the rpoS knock-out biofilms (MBF). Keywords: cell type comparison (biofilms vs planktonic cells, wild type vs rpoS knock-out strains)

2008-05-23 | GSE7885 | GEO

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