Escherichia coli K-12
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ABSTRACT:
PROVIDER: PRJNA107353 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Substrains in Escherichia coli K-12 MG1655 can possess various swimming motility, which is mostly resulted from different expression levels of flhDC. Here, we studied the swimming motility of two MG1655 substrains, CY562 and CY570. Our results showed that CY562 had no insertion at the promoter region of flhDC and possessed no swimming motility. In contrast, CY570 had an IS-element insertion at the promoter region of flhDC and showed a hyper-motile phenotype. Transcriptomic data suggest that expression of flhDC and the other known flagella genes was much lower in CY562 than that in CY570. Moreover, CY562 possessed higher expression levels for genes involved in stress response, especially acid-stress response, than CY570. Consistently, CY562 showed a higher survival rate under acid stress than CY570. Our data indicate that there are mechanisms conversely regulating motility and stress response in E. coli.
2021-11-15 | GSE165438 | GEO
Project description:This series presents normalized gene expression profiles of three Escherichia coli K-12 MG1655-derived strains (pygYFP, Y5, and Y6). Strains Y5 and Y6 were originally isolated from 3-week-old aging colonies, but RNA for transcriptomic profiling was extracted from 7-day-old colonies regrown under identical conditions. All samples were hybridized to the NimbleGen GPL9088 one-color microarray platform, and processed values correspond to RMA-normalized, non-log2 intensities. These data compare the parental strain to two evolved isolates carrying distinct regulatory and stress-response mutations, and can be used to study diversification and adaptive strategies emerging in aging bacterial colonies.
2026-03-10 | GSE312419 | GEO
Project description:This series presents normalized gene expression profiles of three Escherichia coli K-12 MG1655-derived strains (pygYFP, Y5, and Y6). Strains Y5 and Y6 were originally isolated from 3-week-old aging colonies, but RNA for transcriptomic profiling was extracted from 7-day-old colonies regrown under identical conditions. All samples were hybridized to the NimbleGen GPL9088 one-color microarray platform. Processed values correspond to RMA-normalized, non-log2 intensities. Raw .pair files and the processed matrix for these samples are provided. These data complement Series 1 and constitute a second biological replicate (B2) for transcriptomic analysis of the parental strain and two evolved isolates carrying distinct mutations affecting regulatory and stress-response pathways in aging bacterial colonies.
2026-03-10 | GSE312426 | GEO
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 ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The ∆hns/∆stpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure
2013-06-20 | GSE41186 | GEO
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆arcA mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the ArcA protein. The results are further 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 | GSE46412 | GEO
Project description:Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.
2019-06-17 | GSE126710 | GEO
Project description:The gene expression profile of E. coli K-12 MG1655 grown in minimal medium supplemented with elevated copper concentrations (as copper-glycine) has been analysed using whole genome oligonucleotide microarrays. “Pool” RNA was isolated from five independently grown 50ml DMA cultures of E. coli K-12 MG1655. “Test” RNA was isolated from three independently grown 50ml DMA cultures of E. coli K-12 MG1655, for each growth condition (no added CuSO4, or supplemented with either 0.75mM or 2mM copper glycine). A sample of each culture was taken at mid to late exponential growth phase at OD600 0.8 (measured using a Pharmacia Biotech Ultrospec 2000 in a cuvette with a path length of 10mm). Keywords: dose response
2004-09-22 | GSE1780 | GEO
Project description:Protein extract of Escherichia coli K-12 MG1655 was separated by RPLC on a Waters NanoAquity system with a custom packed C5 column and analyzed by an LTQ Orbitrap Velos mass spectrometry. Parent spectra were collected at a 60000 resolution and the top 4 ions were selected for LC-MS/MS analysis in which the resolution was 60000 and the alternating fragmentation mode was used. In total, 2027 collision-induced dissociation (CID) and 2027 electron-transfer dissociation (ETD) top-down MS/MS spectra were collected.
2018-04-04 | MSV000082237 | MassIVE
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