Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA95671 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:E. coli Transcriptome Dynamics during the Transition from Aerobic to Micro-aerobic Conditions
| PRJNA98839 | ENA
Project description:In Escherichia coli, Lon is an ATP-dependent protease which degrades misfolded proteins and certain rapidly-degraded regulatory proteins. Given that oxidatively damaged proteins are generally degraded rather than repaired, we anticipated that Lon deficient cells would exhibit decreased viability during aerobic, but not anaerobic, carbon starvation. We found that the opposite actually occurs. Wild-type and Lon deficient cells survived equally well under aerobic conditions, but Lon deficient cells died more rapidly than the wild-type under anaerobiosis. Microarray analysis revealed that genes of the Clp family of ATP-dependent proteases were induced during aerobic growth but not during anaerobic growth. Thus, Clp may compensate for loss of Lon when cells are in an oxygen containing atmosphere. Under anaerobic carbon starvation conditions, Lon must be active to support survival. Keywords: Other
2007-11-01 | GSE6609 | GEO
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 M-bM-^HM-^FarcA 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 Mapping of occupancy of ArcA in the genome of Escherchia coli MG1655 K-12 during anaerobic fermentation and aerobic respiration. Immunoprecipitated DNA compared to INPUT for each sample.
2013-10-17 | E-GEOD-46413 | biostudies-arrayexpress
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
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ?fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. WT strains were grown under aerobic and anaerobic growth conditions. A six chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 WT (aerobic and anaerobic) and two separate cultures of the ?fnr mutant strain (anaerobic). Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 with eight 60-mer probes per gene, with each probe represented twice on the array.
2013-06-20 | E-GEOD-41189 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ?fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. WT strains were grown under aerobic and anaerobic growth conditions.
2013-06-20 | GSE41189 | GEO
Project description:The changes in protein composition of E. coli were studied in a global proteomic approach for aerobic growth without or with fumarate as carbon source (glycerol + O2, fumarate + O2, respectively) and anaerobic growth without or with fumarate as carbon source (glycerol + DMSO, glycerol + DMSO + fumarate, respectively). The experiments should unravel the changes in response to fumarate under aerobic (i) and anaerobic (ii) conditions, and more generally (iii) the fumarate proteome under aerobic versus anaerobic conditions. Fumarate was used as the C4DC due to its capability to support aerobic and anaerobic growth, and glycerol was used as the alternative carbon source that exerts no or only weak carbon catabolite repression.
2019-11-20 | PXD011760 | Pride
Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of an anaerobic environment on E. coli O157:H7, global transcript levels of strain EDL933 cells grown aerobically were compared to cells grown anaerobically using microarrays. Eight independent RNA samples from aerobic cultures were paired with eight independent RNA samples from anaerobic cultures for hybridization to eight two-color microarrays. For four arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.
2010-12-01 | E-GEOD-13301 | biostudies-arrayexpress
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 M-CM-^_ subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a M-bM-^HM-^Ffnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The M-bM-^HM-^Fhns/M-bM-^HM-^FstpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure Mapping of occupancy of FNR, NNS, IHF and M-CM-^_ of RNAP in the genome of Escherchia coli MG1655 K-12 under aerobic or anaerobic growth conditions. Immunoprecipitated DNA compared to INPUT for each sample.
2013-06-20 | E-GEOD-41186 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆hns/∆stpA strain from exponental growth under aerobic and anaerobic growth conditions. The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding.
2013-06-20 | GSE46144 | GEO