Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression analysis of Escherichia coli MG1655 K-12 WT and ∆fnr mutant

ABSTRACT: 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.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655star Escherichia coli K-12

PROVIDER: GSE41189 | GEO | 2013/06/20

SECONDARY ACCESSION(S): PRJNA176150

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Chip-chip from Escherichia coli MG1655 K-12, WT and ∆fnr strains

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

Expression analysis of Escherichia coli MG1655 K-12 WT and M-bM-^HM-^Ffnr mutant

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

Expression analysis of Escherichia coli MG1655 K-12 ∆hns/∆stpA from aerobic and anaerobic growth conditions

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

Expression analysis of Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA from aerobic and anaerobic growth conditions

Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA 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. A four chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA mutant strain under aerobic and anaerobic growth conditions. Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 using a high-density tiling array consisting of ~385,000 60mer probes spaced every 12 bp.

2013-06-20 | E-GEOD-46144 | biostudies-arrayexpress

Chip-chip from Escherichia coli MG1655 K-12, WT and M-bM-^HM-^Ffnr strains

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

High-throughput Solexa sequencing of total RNA from Escherichia coli wild type and ∆fnr strain (PK4854)

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.

2013-06-20 | GSE41190 | GEO

ArcA Chip-chip from Escherichia coli MG1655 K-12, WT and ∆arcA strains

2013-10-17 | GSE46413 | GEO

FNR- vs WT in anoxic conditions

2007-01-05 | GSE3657 | GEO

ArcA Chip-chip from Escherichia coli MG1655 K-12, WT and M-bM-^HM-^FarcA strains

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

FNR- vs WT in anoxic conditions

Project description:Salmonella enterica var. Typhimurium (S. Typhimurium) is a Gram-negative, facultative intracellular pathogen that infects the intestinal tracts of humans and animals. In the host, S. Typhimurium encounters a wide range of oxygen concentrations going from oxic conditions in the stomach to near anoxic conditions in the distal sigmoid colon-rectal junction. In Escherichia coli, FNR (Fumarate Nitrate Reductase) is one of the main regulatory proteins involved in oxygen sensing and in controlling the transcription of the genes required for the aerobic/anaerobic transition.. However, the role of FNR in S. Typhimurium is largely unknown. To assess its role in S. Typhimurium, we constructed an FNR- mutant (NC983) in the pathogenic wild-type (WT) strain, ATCC14028s. The WT and the fnr- mutant strains were grown under anaerobic conditions in a Coy Anaerobic Chamber. Total RNAs were isolated when the cultures reached an OD600 of 0.3 (mid-log). Microarray slides were used to compare the global expression patterns of the two strains (i.e., 14028s vs. NC983). On each slides there were three replicas of the Salmonella genome and we swapped dyes, thus having a total of six replicates for each gene.

2010-07-01 | E-GEOD-3657 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data