Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff

ABSTRACT: Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff

PROVIDER: PRJNA661297 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff

Project description:mRNA half-life profiling in the bacterium Caulobacter crescentus was preformed by shutting of transcription with the antibiotic rifampicin, and following mRNA abundance at 1, 2, 4, 8, and 15 minutes post rifampicin. All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium. Two biological replicates time coursees were collected from independent starter cultures.

2020-09-04 | GSE157432 | GEO

Global RNA half lives in cyanobacteria

Project description:We calculated global RNA half lives for all genes in the cyanobacteria Synechococcus sp. strain PCC 7002. Samples from three replicates of the WT strain were taken before and following the addition of the antibiotic rifampicin to stop nascent transcription. RNA spike-ins were added for normalization and using the number of RNA-sequencing reads we were able to calculate half lives for genes, transcripts, and for each position on the genome.

2019-01-01 | GSE109174 | GEO

Cell cycle mRNA half-life profiling.

Project description:mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in synchronized cells collected from different stages of the cell cycle including swarmer cells, stalk cells (45 min post synchrony), and predivisional cells (90 min post synchrony). For each cell population, transcription was disrupted by the antibiotic rifampicin, and RNA samples were collected at different time points to measure the mRNA half-lives.

2023-04-03 | GSE228593 | GEO

Global RNA half lives in cyanobacteria

Project description:Global RNA half lives in cyanobacteria

| PRJNA429921 | ENA

WT and RNE∆IDR mRNA half-life profiling in Sinorhizobium meliloti.

Project description:WT and RNE∆IDR strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq. Wild type(WT) was compared to RNE∆IDR strain.

2023-12-25 | GSE251703 | GEO

analysis of the C. albicans mRNA half-lives

Project description:This work aimed at analysing mRNA half lives in drug resistant and in drug sensitive strains of C. albicans (Gu4 and Gu5 azole susceptible and resistant clinical isolates (franz et al., 1999)), using the transcriptional inhibitor thiolutine.

2011-10-01 | E-TABM-1179 | biostudies-arrayexpress

WT, ∆rhlB and ∆rppH mRNA half-life profiling.

Project description:WT, ∆rhlB and ∆rppH strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq. Wild type(WT) was compared to ∆rhlB (deleted RNA helicase RhlB gene) and ∆rppH (deleted RppH gene) strains

2023-04-03 | GSE228592 | GEO

Retapamullin and Chloramphenicol treated mRNA half-life profiling.

Project description:mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in cells that were inhibited in translation initiation (retapamullin) or elongation (chloramphenicol) by shutting of transcription with the antibiotic rifampicin, and following mRNA abundance at 1, 2, 4, 8, and 15 minutes post rifampicin. All RNA measurements were performed on cells grown to mid-log in M2G minimal growth medium. Two biological replicates time coursees were collected from independent starter cultures.

2023-04-03 | GSE228591 | GEO

Half-lives mRNA analysis of Stenotrophomonas maltophilia D457 and rng-deficient mutant

Project description:We calculated half-life values of mRNAs quantified by RNA-Seq by a suitable method of normalization. We determined the half-lives of more than 2200 mRNAs in the Stenotrophomonas maltophilia D457 wild-type strain and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient mutant respectively. We found an overall enhancement of half-life times of mRNAs when the gene encoding RNase G is lacking, showing that many RNAs are targets of RNase G in S. maltophilia. For achieving such goal, we propose a method for the normalization of RNA-Seq based studies on global bacterial mRNA decay.

2017-09-06 | GSE103467 | GEO

Global analysis of mRNA isoform half-lives: identification of stabilizing and destabilizing elements in yeast

Project description:We measured half-lives of 21,248 mRNA 3’ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, the half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A) binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilization and stabilization elements are linked to the degree to which the poly(A) tail can engage in double-stranded structures. Isoforms engineered to fold into 3’ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at the 3’ ends are a major determinant of mRNA stability. Half-lives of 21,248 mRNA 3’ isoforms in yeast were measured by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process.

2014-04-02 | E-GEOD-52286 | 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