Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of MG1655 Escherichia coli (Wild-type, and mutants lacking the glucose metabolism regulator TmaR) experiencing short- & long-term N starvation and following treatment with rifampicin during long-term N starvation in Gutnick minimal media

ABSTRACT: RNA-seq was carried out to compare the transcriptomes of wild-type MG1655 E coli with mutants lacking the glucose metabolism regulator TmaR , in bacteria that had been exposed to short-term (3hr) and long-term (24hr) nitrogen starvation in Gutnick minimal media. A rifampicin-chase experiment was performed following long-term (24hr) nitrogen starvation, with 150ug/ml rifampicin added at N-24, with samples taken 15 and 60 minutes following treatment. TmaR is required for the formation of Hfq foci, a novel sub-cellular feature that forms during long-term nitrogen starvation. The aim of this work was to use the mutant lacking TmaR to understand the functional role of the Hfq foci, and whether they play a role in sRNA stability during long-term nitrogen starvation.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Escherichia coli K-12

SUBMITTER: Josh McQuail

PROVIDER: E-MTAB-15469 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analysis of MG1655 Escherichia coli (Wild-type and mutant lacking the RNA chaperone Hfq) experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA-seq was carried out to compare the transcriptomes of wild-type MG1655 E coli with mutant lacking the prominent RNA chaperone, Hfq, in bacteria that had been exposed to short-term (20min, N-) and long-term (24hr, N-24) nitrogen starvation, and following replenishment of nitrogen to long-term starved bacteria (~2hrs, N-24+2) in Gutnick minimal media. The aim of this was to understand what the regulatory contribution of Hfq was to bacteria experiencing nitrogen starvation.

2023-12-01 | E-MTAB-13527 | biostudies-arrayexpress

RNA-seq analysis of MG1655 Escherichia coli (Wild-type and mutant lacking the small regulatory RNA SdsR) experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA-seq was carried out to compare the transcriptomes of wild-type MG1655 E coli with mutant lacking the prominent sRNA, SdsR, in bacteria that had been exposed to long-term (24hr) nitrogen starvation in Gutnick minimal media. The aim of this was to understand what the regulatory contribution of SdsR was to bacteria experiencing long-term nitrogen starvation.

2023-12-01 | E-MTAB-13402 | biostudies-arrayexpress

RNA-seq analysis of BW25113 Escherichia coli (Wild-type, and mutants lacking the glucose metabolism regulator TmaR or the RNA Chaperone Hfq) experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA-seq was carried out to compare the transcriptomes of wild-type BW25113 E coli with mutants lacking either the glucose metabolism regulator TmaR or the ubiquitous RNA chaperone Hfq, in bacteria that had been exposed to long-term (24hr) nitrogen starvation in Gutnick minimal media. All strains also contain the empty plasmid pBAD18, as this was initial performed alongside a larger RNA-seq study - as such the WT and Hfq mutant are previously available in E-MTAB-14054. TmaR is also required for the formation of Hfq foci, a novel sub-cellular feature that forms during long-term nitrogen starvation. The aim of this work was to use the mutant lacking TmaR to understand the functional role of the Hfq foci during long-term nitrogen starvation.

2025-12-31 | E-MTAB-14999 | biostudies-arrayexpress

RNA-seq analysis of BW25113 Escherichia coli (Wild-type, mutant lacking the RNA Chaperone Hfq, and strains complemented with Wild-type and point mutants of Hfq) experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA-seq was carried out to compare the transcriptomes of wild-type BW25113 E coli with a mutant lacking the ubiquitous RNA chaperone Hfq, in bacteria that had been exposed to long-term (24hr) nitrogen starvation in Gutnick minimal media. The mutation was also complemented with wild-type Hfq or point mutants of Hfq (Q8A, V22A & G34A), provided by the arabinose inducible pBAD plasmid. The aim of this was to understand the effect of different point mutations of Hfq on the transcriptome, and specifically sRNA stability under physiological conditions.

2024-12-31 | E-MTAB-14054 | biostudies-arrayexpress

RNA-Seq of BW25113 Escherichia coli (wild-type and a mutant lacking yeaG) experiencing initial and sustained nitrogen starvation in Gutnick minimal media

Project description:RNA-seq was carried out to compare the transcriptomes of wild-type BW25133 E coli with a mutant lacking the conserved serine/threonine kinase, YeaG, with the aim of understanding how YeaG contributes to the transcriptional response to sustained nitrogen starvation, and identify pathways affected by YeaG. We also compare the wild-type transcriptome during nitrogen-replete, following nitrogen starvation, and under 24 h of sustained nitrogen starvation to identify pathways involved in the response to nitrogen run out, and also in adaptation to sustained nitrogen starvation.

2018-06-04 | E-MTAB-6481 | biostudies-arrayexpress

RNA-seq data of E. coli MG1655 WT and hfq knockout strains during short and long-term nitrogen starvation.

Project description:RNA-seq data to compare the transcriptomes of wild-type and hfq mutant E. coli strain MG1655 experiencing nitrogen starvation for 20 min (N-) and 24 hours (N-24). To look at the RNA expression profile of E. coli during Nitrogen starvation and comparing how this changes in bacteria lacking Hfq at two specific timepoints; short-term Nitrogen starvation, N- (20min into starvation), and long-term Nitrogen starvation, N-24 (24hours into starvation).

2023-12-29 | E-MTAB-12794 | biostudies-arrayexpress

Whole-cell differential proteomics analysis of MG1655 Escherichia coli (Wild-type and mutants lacking the small regulatory RNA SdsR, OxyS or ZbiJ, or the RNA Chaperone Hfq) experiencing long-term nitrogen starvation in Gutnick minimal media.

Project description:Proteomics was carried out to compare the proteomes of wild-type MG1655 E coli with mutants lacking either prominent sRNA, SdsR, OxyS or ZbiJ, or lacking the ubiquitous RNA chaperone proteins hfq, in bacteria that had been exposure to long-term (24hr) nitrogen starvation in Gutnick minimal media. The aim of this was to understand what the regulatory contribution of these three sRNA was to bacteria experiencing long-term nitrogen starvation.

2024-05-24 | PXD045656 | Pride

A PP2A-Pab1-mediated crosstalk between TORC1 & TORC2 regulates the differentiation response in fission yeast

Project description:RNA-sequencing of S. pombe wild type, ppa1 mutants, and tor1 mutants, grown under condition of normal nitrogen and under nitrogen starvation.

2016-10-31 | E-MTAB-4106 | biostudies-arrayexpress

nitrogen starvation and re-supply-Improving the nitrogen use efficiency : from model plant to crop species.

Project description:gnp3-b4_nitrogen_starvation - nitrogen starvation and re-supply - What are the transcriptomic short- and long-term plant responses to nitrogen starvation and nitrogen re-supply? - WS Arabidopsis ecotype were grown on 6mM nitrate as sole nitrogen source during 35 days under short days . At T0, plants were then starved for nitrate for 10 days and root and shoot samples were harvested separately 2 and 10 days after treatment (T2, T10). Then, nitrate (6 mM) was re-supplied for 1 and 24 hours (T+1, T+24). Keywords: time course

2007-06-20 | GSE8031 | GEO

Multiple roles of RNase Y in Streptococcus pyogenes mRNA metabolism

Project description:Streptococcus pyogenes (Group A streptococcus, GAS) is an important human pathogen that causes a variety of infectious diseases and sequelae. Recent studies showed virulence factor expression was controlled at multiple levels, including the post-transcriptional regulation. In this study, we examined the global half-lives of S. pyogenes mRNAs and explored the role RNase Y played in mRNA metabolism with microarray analysis. key word: genetic modification Streptococcus pyogenes NZ131 wild-type cells and ?rny strains were grown in C-medium until late exponential phase. Rifampicin was added to the cell culture and samples were collected before and after rifampicin addition. The transcriptional profile of the whole genome before and after rifampicin addition was examined with microarray. Please note that mRNA decay assay resulted in considerable variations in the datasets. Samples were taken after rifampicin addition and subsequent incubation for different time intervals. During that time no new RNA is produced and the remaining RNA is degraded to various degrees.

2013-02-01 | E-GEOD-40198 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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