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Transcriptome analysis of E.coli MG1655 under multiple growth conditions

ABSTRACT: Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and nitrogen-limiting condition.

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

PROVIDER: GSE15534 | GEO | 2009/11/04

SECONDARY ACCESSION(S): PRJNA115961

REPOSITORIES: GEO

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Transcriptome analysis of E.coli MG1655 under multiple growth conditions

Project description:Investigation of comprehensive information about the expression level of RNA transcripts across the entire E.coli genome in mulitple growth conditions, including log-phase; stationary phase, heat shock and nitrogen-limiting condition. A fourteen chip study using total RNA recovered from four separate culture conditions of E.coli K12 MG1655. E.coli strains were harvested at mid-exponential phase with exception of stationary phase experiments. 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 (NimbleGen). Experiments were conducted as three or more biological replicates (different cultures)

2009-11-03 | E-GEOD-15534 | biostudies-arrayexpress

DNA microarray analysis of E.coli K12 MG1655 exposed to prolonged stationary phase

Project description:This study explores the effects of prolonged stationary phase, on whole genome expression of Escherichia coli. In summary these results imply that prolonged stationary phase cells have shown less growth rate compared to fresh cells due to the low abundance of transcripts for translation initiation factor infC, and for all the seven rrn operons of 5S, 16S, 23S ribosomal RNA which further delayed in protein synthesis leading to low biomass in prolonged stationary phase cells. 28 days old E.coli cells were grown in the presence of LB broth and LB broth supplemented with 10% v/v glycerol. RNA was extracted from these samples, cDNA was prepared, fragmented cDNA was labled with labeling reagent and hybridized with Affymetrix E.coli2.0 genome array chips.Data was analysed to get the effect of glycerol on E.coli gene expression

2013-09-12 | E-GEOD-50828 | biostudies-arrayexpress

Transcription profiling of E.coli Fis knockout strain

Project description:Fis is a nucleoid-associated protein in E. coli that is abundant during early logarithmic growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild type strains during early log, mid log, late log, and stationary growth phases. We used microarrays to detail the global impact of Fis on gene expression in Escherichia coli Experiment Overall Design: E.coli cells were were grown and samples were taken at different times during growth: 90 min (early logarithmic phase), 150 min (mid-logarithmic phase), 240 min (late logarithmic phase), and 360 min (early stationary phase) for RNA extraction and hybridization on Affymetrix microarrays. This was done in triplicate and the raw data was analyzed using Microarray Analysis Suite version 5.0 (Affymetrix).

2008-06-15 | E-GEOD-7379 | biostudies-arrayexpress

Transcription profiling of E.coli wild type (Fis+) strain

2008-06-15 | E-GEOD-7380 | biostudies-arrayexpress

DNA microarray analysis of E.coli K12 MG1655 exposed to prolonged stationary phase

2013-09-12 | GSE50828 | GEO

Transcriptome analysis of Thermotoga maritima under multiple growth conditions [tiling array]

2013-08-02 | GSE37391 | GEO

RNA-Seq analysis of E.coli, under multiple growth conditions

Project description:The goal of the study is to obtain rna concentrations of E.coli under different growth conditions including growth phase carbon source and salt stresses of Mg+2 and Na+

2017-01-27 | GSE94117 | GEO

Transcriptome analysis of Thermotoga maritima under multiple growth conditions [tiling array]

Project description:Investigation of transcripts (boundary, level, etc.) across the entire T. maritima genome in mulitple growth conditions, including logphase, late exponential, heat shock and hydrogen inhibited conditions. The new genome annotation has been approved by Genbank [CP004077, pending release of the manuscript]. A fourteen array expression profiling study was performed using total RNA from four distinct growth conditions collected under maltose minimal media.

2013-08-02 | E-GEOD-37391 | biostudies-arrayexpress

Transcription profiling of stationary phase E.coli wild type and crl::cat mutant strains to identify Crl-regulated genes

Project description:We wished to identify Crl-regulated genes in stationary phase in E.coli, and whether those overlap with the previously identified regulon of RpoS. Therefore wildtype E.coli (MC4100) and its isogenic crl::cat mutant were grown at 30oC. Total RNA was extracted at on OD (578nm) of 4 (during entry into stationary phase) and then the analysis proceeded as described in detail in the protocoles. The experiment was repeated three times and the results from those experiments are presented here.

2007-01-01 | E-MEXP-720 | biostudies-arrayexpress

Comparison of gene expression of L. reuteri ATCC 55730 at different growth phase in LDMIII medium

Project description:Comparison of gene expression between L. reuteri ATCC 55730 in LDMIII between early log phase (T8), late log phase (T12) or early stationary phase phase (T16) or late stationary phase (T24)

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