Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Sequencing of wild type and RNA polymerase mutant (rpoCA494V) strains of Escherichia coli

ABSTRACT: RNA Sequencing of wild type Eschrichia coli and a RNA polymerase mutant isolated from deep stationary phase

ORGANISM(S): Escherichia coli

PROVIDER: GSE141883 | GEO | 2020/04/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Global timeospatial map of RNA polymerase in Escherichia coli

Project description:To investigate the relationship between RNA polymerase binding and transcription ChIP-seq on the common house-keeping SigmaD and RNA polymerase beta subunit were coupled with RNA-seq at various growth phases of Escherichia coli in rich media.

2020-07-06 | GSE153815 | GEO

Metabolomics in Escherichia coli mutant strains

Project description:Escherichia coli mutant strains were prepared for metabolomics analysis.

2019-07-09 | ST001321 | MetabolomicsWorkbench

Natural RNA polymerase aptamers regulate transcription in E. coli [SELEX]

Project description:In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP) we deep-sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches we characterized a subset of RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing growth conditions. The mechanism of iRAPs involves active uncoupling of transcription and translation, making the nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.

2017-06-01 | GSE98659 | GEO

Natural RNA polymerase aptamers regulate transcription in E. coli [3' RACE]

2017-06-01 | GSE98660 | GEO

The small transcriptome of Escherichia coli in exponential and stationary phase

Project description:We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.

2020-11-21 | GSE161907 | GEO

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

Transcription profiling of E. coli W3110 wild type and rpoZ mutant cells to distinguish between the genes expressed either in the presence or absence of RNA polymerase omega subunit during log phase

Project description:Comparison of transcript profiles of E. coli W3110 wild-type and rpoZ mutant cells to distinguish between the genes expressed either in the presence or absence of RNA polymerase omega subunit during log phase. Comparison of transcript profiles of E. coli rpoZ mutant cells with or without overproduction of episomal rpoD during the mid log, late log phases and also during transition to stationary phase.

2007-08-01 | E-MEXP-942 | biostudies-arrayexpress

RNA Sequencing of wild type and RNA polymerase mutant (rpoCA494V) strains of Escherichia coli

Project description:RNA Sequencing of wild type and RNA polymerase mutant (rpoCA494V) strains of Escherichia coli

| PRJNA595088 | ENA

Escherichia coli RNA-Seq

Project description:The goal of this study is to compare gene expression data for a well known model organism (Escherichia coli) using different technologies (NGS here, microarray from GSE48776). mRNA profiles of Wild Type and two Mutant Strains (ydcR (b1439) MUTANT and yjiR (b4340) MUTANT), growth in minimal medium, were generated by deep sequencing, in triplicate, using Illumina MiSeq.

2013-07-12 | E-GEOD-48829 | biostudies-arrayexpress

Escherichia coli: untreated versus 5-azacytidine-treated expression profiles

Project description:DNA microarray experiments were used to compare gene expression profiles of untreated and 5-azacytidine treated Escherichia coli at both logarithmic phase and early stationary phase The goal was to determine the effect of cytosine DNA methylation loss on gene expression (5-azacytidine is a methylation inhibitor)

2016-09-24 | GSE73707 | GEO

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