Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Phylogenetic analysis of intron retention in vertebrates

PROVIDER: PRJNA350712 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5457065_1.fastq.gz	Fastqsanger.gz
	SRR5457065_2.fastq.gz	Fastqsanger.gz
	SRR5457056_1.fastq.gz	Fastqsanger.gz
	SRR5457056_2.fastq.gz	Fastqsanger.gz
	SRR5457066_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Intron retention analysis using isogrowth profiling

Project description:Intron retention analysis using isogrowth profiling

| PRJNA648363 | ENA

Spontaneous mutations in FgSAD1 suppress the growth defect of the Fgprp4 mutant by affecting tri-snRNP stability and its docking in Fusarium graminearum

Project description:Purpose: For detecting splicing defects in wild type PH-1 and sector S139 and transformant D10. Our results showed that S139 and D10 had similar intron retention levels (un-spliced introns). The intron retention levels in S139 were significantly higher than those in PH-1 (P<0.001,t-test). For the 15,211 introns in the 6,995 genes expressed across two strains, approximately 25% of them had an over 2-fold intron retention rate in comparison with the intron retention rate in PH-1, indicating splicing defects in S139 and D10.

2019-05-15 | GSE131206 | GEO

Project description:Orchestrated intron retention regulates normal granulocyte differentiation

| PRJNA209615 | ENA

Alternative splicing and the epigenome in CML remission [RNA-Seq]

Project description:Transcriptomic and epigenomic profiling of matched CML diagnosis/remission samples revealed a reconfiguration of gene expression and DNA methylation at remission exhibiting patterns similar to those observed in healthy individuals. In contrast, alternative splicing retains chronic phase-like abnormal patterns. Most dramatic dissimilarities between remission and healthy control samples were observed in intron retention. While reduced DNA methylation around splice sites could explain increased intron retention at diagnosis, maintenance of high intron retention levels at remission has other causes, such as reduced splicing factor expression and histone modifications.

2020-06-30 | GSE144119 | GEO

Alternative splicing and the epigenome in CML remission [WGBS]

2020-12-19 | GSE163522 | GEO

Gene expression and intron retention analysis of ZCRB1-knockdown human cells

Project description:Gene expression and intron retention analysis of ZCRB1-knockdown human cells

| PRJNA758028 | ENA

Gene expression and intron retention analysis of 15.5K-knockdown human cells

Project description:Gene expression and intron retention analysis of 15.5K-knockdown human cells

| PRJNA757717 | ENA

Gene expression and intron retention analysis of bktRNA1-depleted human cells

Project description:Gene expression and intron retention analysis of bktRNA1-depleted human cells

| PRJNA673422 | ENA

Intron retention analysis using isogrowth profiling

Project description:We present an analysis of intron retention under stress from two different drugs and their combinations in yeast Saccharomyces cerevisiae. We previously established isogrowth profiling, a method to abstract the non-specific effects of growth rate inhibition from the specific effect of perturbation by a small molecule: two drugs are used at varied ratios, but at fixed overall growth inhibition. Here, cycloheximide and LiCl were used at seven different ratios along the 50% growth inhibition isobole and the total ribodepleted RNA was sequenced. This allowed us to gauge the changes in intron retention due to the used drugs, while ensuring that the effects are not caused by growth inhibition. We found a prominent increase in intron retention under LiCl treatment that preferentially affects introns contained in the transcripts of ribosomal proteins.

2022-02-15 | GSE155060 | GEO

Integrating Gene Expression and Splicing Dynamics Across Dose-Response Oxidative Modulators

Project description:Toxicological risk assessment increasingly utilizes transcriptomics to derive point of departure (POD) and modes of action (MOA) for chemicals. One essential biological process that allows a single gene to generate several different RNA isoforms is called alternative splicing. To comprehensively assess the role of splicing dysregulation in toxicological evaluation and elucidate its potential as a complementary endpoint, we performed RNA-seq on A549 cells treated with five oxidative stress modulators across a wide dose range. Differential gene expression (DGE) showed limited pathway enrichment except at high concentrations. However, alternative splicing analysis revealed variable intron retention events affecting diverse pathways for all chemicals in the absence of significant expression changes. For instance, diazinon elicited negligible gene expression changes but progressive increase in the number of intron retention events, suggesting splicing alterations precede expression responses. Benchmarkdose modeling of intron retention data highlighted relevant pathways overlooked by expression analysis. Systematic integration of splicing datasets should be a useful addition to the toxicogenomic toolkit. Combining both modalities paint amore complete picture of transcriptomic dose-responses. Overall, evaluating intron retention dynamics afforded by toxicogenomics may provide biomarkers that can enhance chemical risk assessment and regulatory decision making. This work highlights splicing-aware toxicogenomics as a possible additional tool for examining cellular responses.

2024-05-15 | GSE241672 | 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