Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Determination of mRNA half-lives in embryonic mouse skin

ABSTRACT: Determination of mRNA half-lives in embryonic mouse skin

PROVIDER: PRJEB21639 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2025900_1.fastq.gz	Fastqsanger.gz
	ERR2025900_2.fastq.gz	Fastqsanger.gz
	ERR2025901_1.fastq.gz	Fastqsanger.gz
	ERR2025901_2.fastq.gz	Fastqsanger.gz
	ERR2025902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Determination of mRNA half-lives in embryonic mouse skin

Project description:Embryonic mouse skin samples were halved, one half separated into epidermis and dermis and RNA isolated, and the other half immersed in medium containing Actinomycin D (Act D) to halt transcription. After 30, 60 or 120 minutes at 37 degrees C the Actinomycin D treated samples were separated into epidermis and dermis and RNA isolated from these. Resulting RNA samples were sequenced to quantify transcript abundances.

2017-07-14 | E-MTAB-5841 | biostudies-arrayexpress

Global RNA half lives in cyanobacteria

Project description:Global RNA half lives in cyanobacteria

| PRJNA429921 | ENA

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

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

Caulobacter crescentus mRNA half-lives by rifampicin transcription shutoff

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

| PRJNA661297 | ENA

Determining mRNA half-lives on a transcriptome-wide scale

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

| PRJNA416702 | ENA

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

Half-life determination for human B-cells (BL41)

Project description:RNA was labeled in BL41 cells by culturing cells for 60 min in media containing 100µM 4sU. Tc-RNA was separated into nt- and p-RNA. All three RNA subsets were subjected to microarray analysis. Only probe sets providing present calls in all RNA samples/subsets were included into the analysis We used microarrays to determine half-lives of mRNAs expressed in BL41 cells Keywords: Determination of mRNA half-life in human B-cells

2009-09-30 | GSE9973 | GEO

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

2014-04-02 | GSE52286 | GEO