Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Measurement of mRNA stability during transcriptional memory in mutants for RNA degradation

ABSTRACT: Measurement of mRNA stability during transcriptional memory in mutants for RNA degradation

PROVIDER: PRJNA903499 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22351718.fastq.gz	Fastqsanger.gz
	SRR22351719.fastq.gz	Fastqsanger.gz
	SRR22351720.fastq.gz	Fastqsanger.gz
	SRR22351721.fastq.gz	Fastqsanger.gz
	SRR22351722.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Measurement of mRNA stability during transcriptional memory in mutants for RNA degradation

Project description:Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, we investigate the contribution of cytoplasmic RNA decay to this process, we investigate global changes in mRNA turnover in ski2∆ (component of the cytoplasmic 3’-5’exosome) and xrn1∆ (cytoplasmic 5’-3’exonuclease) strains in S. cerevisiae.

2023-01-09 | GSE218400 | GEO

Measurement of the degradation rate of alphaviral RNA in BHK-21 cells

Project description:Measurement of the degradation rate of alphaviral RNA in BHK-21 cells

| PRJNA985721 | ENA

S100A4 mRNA-protein relationship uncovered by measurement noise reduction

Project description:Intrinsic biological fluctuation and/or measurement error can obscure the association of gene expression patterns between RNA and protein levels. Appropriate normalisation of reverse-transcription quantitative PCR (RT-qPCR) data can reduce technical noise in transcript measurement, thus uncovering such relationships. The accuracy of gene expression measurement is often challenged in the context of cancer due to its genetic instability and ‘splicing weakness’. Here we sequenced the poly(A) cancer transcriptome of canine osteosarcoma using mRNA-Seq. Expressed sequences were resolved at the level of two consecutive exons to enable the design of exon-border spanning RT-qPCR assays and ranked for stability based on the coefficient of variation (CV). Using the same template type for RT-qPCR validation, i.e. poly(A) RNA, avoided skewing of stability assessment by circular RNAs (circRNAs) and/or rRNA deregulation. The strength of the relationship between mRNA expression of the tumour marker S100A4 and its proportion score of quantitative immunochemistry (qIHC) was introduced as an experimental read-out to fine-tune the normalisation choice. Together with the essential logit transformation of qIHC scores, this approach reduced the noise of measurement as demonstrated by uncovering a highly significant, strong association between mRNA and protein expressions of S100A4 (Spearman's coefficient r = 0.72 (p = 0.006)).

2020-03-26 | GSE147550 | GEO

Sex differences in the role of protein degradation in the hippocampus during memory formation

Project description:This project examined sex differences in the role of degradation-specific protein polyubiquitination in the hippocampus during context fear memory formation in male and female rats.

2021-06-28 | PXD026212 | Pride

Sex differences in the role of protein degradation in the amygdala during fear memory formation

Project description:This project examined sex differences in the role of degradation-specific protein polyubiquitination in the amygdala during context fear memory formation in male and female rats.

2021-09-28 | PXD027544 | Pride

Genetic Measurement of Memory B-cell Recall Using Antibody Repertoire Sequencing

Project description:<p>We developed an improved high throughput sequencing approach to measure the quantities and sequences of the repertoire of antibody heavy chain RNA in a blood sample. Using this approach we analyzed the antibody repertoire in response to yearly vaccinations with influenza vaccines TIV and LAIV in healthy adults in two subsequent years. We determined vaccine response patterns specific to LAIV and TIV and found antibody sequences that were shared between two samples of the same individuals following influenza vaccination in subsequent years, thereby providing a genetic measurement of B-cell memory recall.</p>

| phs000656 | dbGaP

Chemical nucleoside conversion-based measurement of RNA stability by targeted and untargeted mRNA 3´ end sequencing

Project description:Chemical nucleoside conversion-based measurement of RNA stability by targeted and untargeted mRNA 3´ end sequencing

| PRJNA484507 | ENA

Genetic measurement of memory B-cell recall using antibody repertoire sequencing

| phs000656.v1.p1 | EGA

Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

Project description:Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

| PRJNA828122 | ENA

Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

Project description:Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, we perform a genome-wide characterisation of this process and explore the contribution of the nuclear mRNA surveillance (RRP6) to this process. Using S. cerevisiae as a model organism, we investigate changes in mRNA abundance, mRNA stability and chromatin organization. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory.

2023-01-09 | GSE201036 | GEO

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