Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq to profile the alterations in transcript half-lives regarding to ac4C regulation

ABSTRACT: RNA-seq to profile the alterations in transcript half-lives regarding to ac4C regulation

PROVIDER: PRJNA941327 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23716231.fastq.gz	Fastqsanger.gz
	SRR23716232.fastq.gz	Fastqsanger.gz
	SRR23716233.fastq.gz	Fastqsanger.gz
	SRR23716234.fastq.gz	Fastqsanger.gz
	SRR23716235.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

RNA-seq to profile the alterations in transcript half-lives regarding to ac4C regulation

Project description:NAT10-catalyzed N4-acetylcytidine (ac4C) has emerged as a vital post-transcriptional modulator on the coding transcriptome by promoting mRNA stability. To investigate the effect of NAT10-mediated ac4C acetylation modification on RNA stability at the transcriptome scale, we performed high throughput RNA sequencing experiments of control and NAT10 KD hESCs at three time points each with 3 replicates.

2023-08-25 | GSE226751 | GEO

Global RNA half lives in cyanobacteria

Project description:Global RNA half lives in cyanobacteria

| PRJNA429921 | ENA

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

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

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

Determining mRNA half-lives on a transcriptome-wide scale

Project description:Determining mRNA half-lives on a transcriptome-wide scale

| PRJNA416702 | ENA

Determination of mRNA half-lives in embryonic mouse skin

Project description:Determination of mRNA half-lives in embryonic mouse skin

| PRJEB21639 | ENA

Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff

Project description:Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff

| PRJNA661297 | ENA

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

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

2014-04-02 | GSE52286 | GEO