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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profile of an ldhA-pflB- double knockout strain of E. coli BW25113 relative to wild-type

ABSTRACT: Comparison of gene expression profile in E. coli BW25113 wild type and ldhA-pflB- double mutant growing microaerobically in M9 media containing 10 g/L Glucose two samples: wild type and mutant

ORGANISM(S): Escherichia coli

SUBMITTER: Ryan Gill

PROVIDER: E-GEOD-21995 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profile of an ldhA-pflB- double knockout strain of E. coli BW25113 relative to wild-type

Project description:Comparison of gene expression profile in E. coli BW25113 wild type and ldhA-pflB- double mutant growing microaerobically in M9 media containing 10 g/L Glucose

2010-05-26 | GSE21995 | GEO

Transcription profiling of E. coli K12 Bw25113/pCA24N-hha with 2 mM IPTG vs BW25113/pCA24N with 2 mM IPTG

Project description:gene expression profiles by overexpressing Hha from pCA24N-hha using 2 mM IPTG induction in BW25113 wild type suspension cells in LB medium at 37C relative to BW25113 carrying the empty vector plasmid in the same test conditions. Experiment Overall Design: Strains: E. coli K12 BW25113/pCA24N, BW25113/pCA24N-hha Experiment Overall Design: Growth conditions: grow culture in LB medium at 37C to OD600 0.1 and add 2 mM IPTG to induce, and grow to OD600 0.5 to collect cells. RNA was extraction, and gene expression profiles were evaluated.

2008-10-20 | E-GEOD-10116 | biostudies-arrayexpress

E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

2010-01-20 | GSE14064 | GEO

Microarray analysis of RNase I-deficient Escherichia coli versus wild-type BW25113

Project description:The present study investigated the role(s) of RNase I (encoded by the rna gene) in Escherichia coli by comparative gene expression analysis of an rna mutant and the isogenic wild-type E. coli strain BW25113. The transcriptomic analysis aims to provide mechanistic insight into aberrant phenotypes observed in the RNase I-deficient mutant.

2020-01-04 | E-MTAB-6095 | biostudies-arrayexpress

E. coli BW25113 frdC vs. E. coli BW25113 HW2

Project description:Glycerol is an attractive feedstock for biofuels since it accumulates as a byproduct during biodiesel operations; hence, it is interesting to consider converting glycerol to hydrogen using the formate hydrogen lyase system of Escherichia coli which converts pyruvate to hydrogen. Starting with Escherichia coli BW25113 frdC that lacks fumarate reductase to eliminate the negative effect of accumulated hydrogen on glycerol fermentation and by using both adaptive evolution and chemical mutagenesis combined with a selection method based on increased growth on glycerol, we obtained an improved strain, HW2, that produces 20-fold more hydrogen in glycerol medium (0.68 mmol/L/h) compared to that of frdC mutant. HW2 also grows 5-fold faster (0.25 1/h) than BW25113 frdC on glycerol, so it achieves a reasonable growth rate. Corroborating the increase in hydrogen production, glycerol dehydrogenase activity in HW2 increased 4-fold compared to BW25113 frdC. In addition, a whole-transcriptome study revealed that several pathways that would decrease hydrogen yields were repressed in HW2 (fbp, focA, and gatYZ) while a beneficial pathway, eno which encodes enolase was induced.

2010-10-31 | GSE18972 | GEO

Transcriptional responses of Escherichia coli rpoS- BW25113 vs. wild-type BW25113 under 15% ethanol shock in log phase

Project description:RpoS, an alternative sigma factor, is critical for stress response in Escherichia coli.RpoS also acts as a global regulator for stress control of gene expression, and actually dose so in log stage and stationary stage. To further understand the effect of environmental stresses on in ethanologenic strains, DNA microarrys was used to analyze the expression profiles of E. coli and its rpoS mutant strain. BW25113（rpoS-）and BW25113 were selected at log stages and stationary stage of early development for RNA extraction and hybridization on Affymetrix microarrays. To that end, we hand-selected BW25113 and BW25113（rpoS-） according at different treatments: BW25113（rpoS-）at log stage (BW25113(rpoS-) log), BW25113 at log stage (BW25113 log),BW25113（rpoS-）atstationary stage ( BW25113(rpoS-) stationary), BW25113 at stationary stage ( BW25113 stationary)

2010-07-20 | E-GEOD-17526 | biostudies-arrayexpress

E. coli BW25113 ompA mutant vs wild type biofilm and E. coli BW25113 ompA/pCA24N_ompA vs ompA/pCA24N suspension cells

Project description:This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells. Strains: E. coli K-12 BW25113 wild type, ompA mutant Medium: LB Cell type: Biofilm cells grown on glasswool and polystyrene surfaces Time: 15 h Temperature: 37C Strains: BW25113 ompA/pCA24N_ompA and ompA/pCA24N Medium: LB Time: 7 h Temperature: 37C Cell type: suspension cells, induced by 0.1 mM IPTG

2010-11-03 | E-GEOD-14064 | biostudies-arrayexpress

BW25113 Rif pre-treated persister cells vs. stationary phase BW25113 wild-type

Project description:E. coli K-12 BW25113 persister cells generated via rifampicin pre-treatment relative to BW25113 wild-type stationary phase gene expression. Persister cells were generated following exposure to ampicillin 20 ug/mL.

2016-11-20 | GSE34177 | GEO

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

Project description:E. coli K-12 BW25113 persister cells generated via H202 pre-treatment and deletion of rpoS, relative to BW25113 wild-type stationary phase gene expression. Persister cells were generated following exposure to ampicillin 20 ug/mL.

2012-04-03 | GSE34028 | GEO

Transcriptional pattern of E. coli BW25113 and its ptsA, glpK and dhaKLM isogenic mutants growing on DHA (dihydroxyacetone).

Project description:Dihydroxyacetone (DHA) is an attractive molecule produced in a wide range of industries . DHA is found among all the kingdoms as an intermediate of various metabolic pathways and can be used as a carbon source by many organisms. The bacterium Escherichia coli is able to grow on DHA as the sole carbon source albeit at a low growth rate (0.1 h-1). If the topology of DHA metabolic network has been characterized, the function and regulation of the metabolic pathways involved in DHA metabolism remain unsolved. Here, we aimed to better understand DHA metabolism in E. coli BW25113 by exploring its transcriptional pattern on DHA versus glucose. We also studied the pattern of three DHA pathway mutants (dhaKLM, ptsA and glpK).

2019-06-03 | E-MTAB-7666 | biostudies-arrayexpress

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