Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomewide analysis of U1C-dependent alternative splicing

ABSTRACT: To investigate whether U1C plays a role in splicing regulation in human system, we performed siRNA-mediated knockdown of U1C in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing (RNAseq) RNAseq performed with poly(A)+ selected total RNA from U1C-knockdown and control-treated HeLa cells

ORGANISM(S): Homo sapiens

SUBMITTER: Lee-Hsueh Hung

PROVIDER: E-GEOD-42485 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genomewide analysis of U1C-dependent alternative splicing

Project description:To investigate whether U1C plays a role in splicing regulation in human system, we performed siRNA-mediated knockdown of U1C in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing (RNAseq)

2013-09-30 | GSE42485 | GEO

Transcriptome sequencing to systematically detect trans-splicing in human embryonic stem cells

Project description:Trans-splicing occurs post-transcriptionally and generates transcripts that are orderly inconsistent with their corresponding DNA templates. Until recently only exceedingly rare trans-splicing events have been experimentally characterized in the mammalian transcriptomes. Although hundreds to thousands of trans-spliced RNA candidates have been nominated by bioinformatics- or NGS (next-generation sequencing)-based approaches, these candidates unavoidably suffered from potential false positives arising from genetic rearrangement events or in vitro artifacts. Here we develop a pipeline (TSscan) based on NGS transcriptome data to identify trans-splicing in human embryonic stem cells (ESCs). TSscan integrates RNA sequencing data derived from different NGS platforms (i.e., Roche 454, SOLiD, and Illumina) and different human ESC lines (i.e., H1 and H9) as well as several in silico filters to minimize these two types of potential false positives. Our result shows that a tremendous amount of apparent experimental artifacts are indeed present in NGS data, which may be the most major false positives of trans-splicing detection. TSscan totally identified 10 trans-spliced RNA candidates in human ESCs, four of which are experimentally validated to be true. Further experiments reveal that these four events represent differential expression during the transition of pluripotent status to differentiate statuses. Especially, we observe that one event (the trans-spliced isoform of NCRMS), which is also a large intergenic non-coding RNA, tends to be specifically transcribed in ESCs and induced pluripotent stem cells and can conspicuously affect the pluripotency maintenance of ESCs. As far as we know, TSscan is the first pipeline for systematic identification of trans-splicing that utilizes NGS data in the human transcriptome, opening up an important class of post-transcriptional events for comprehensive characterization. human embryonic stem cell H9

2014-02-03 | E-GEOD-30557 | biostudies-arrayexpress

Alternative splicing changes in A. fumigatus sensitized mice

Project description:Dysregulation of alternative splicing of mRNA precursors is known to contribute to numerous human diseases. In this study we carried out the first systematic search for asthma-associated changes in alternative splicing events, using a model of Aspergillus fumigatus (A. fumigatus)-sensitized mice and an exon junction microarray to detect potential changes in alternative splicing. One of the sensitization-associated changes identified in the search was a shift in alternative splicing of the mRNA encoding cFLIP, a modulator of the caspase- mediated extrinsic apoptosis pathway. Expanding these studies to human asthma patients, we discovered a significant decrease in the expression of both cFLIP isoforms in severe corticosteroid- resistant asthmatics. Although it is unclear whether these changes were due solely to differences in alternative splicing, these findings provide evidence that dysregulation of the extrinsic apoptosis pathway is part of the underlying immunopathogenesis of severe refractory asthma. The technical side of the microarray experiment was essentially the Illumina protocol.

2014-01-14 | E-GEOD-28258 | biostudies-arrayexpress

Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

2016-03-14 | E-GEOD-79157 | biostudies-arrayexpress

Next-generation sequencing identifies mRNAs targets that experience significant changes in alternative splicing upon PQBP1 knockdown in mouse embryonic cortical neurons

Project description:PQBP1 is a highly conserved protein closely related to neurodegenerative disorders. We identified PQBP1 as an important alternative splicing effector necessary for maintaining normal neuron functions in the brain. In order to explore PQBP1's functions in alternative splicing regulation and neuronal activities, we systematically profiled the alternative splicing targets of PQBP1 in mouse embryonic cortical neurons by RNA-seq. The mRNAs whose alternative splicing are affected by PQBP1 showed tissue-specific functional enrichment especially in neurite outgrowth, with strong Gene Ontology (GO) enrichments for neuron projection development/morphogenesis, dendrite development and axonogenesis. PQBP1's alternative splicing targets are also functionally enriched in RNA splicing, chromatin modification, and ARF signal transduction. We applied RNA-seq to compare the transcriptomes of mock and PQBP1 knockdown mouse embryonic cortical neuron samples.

2013-03-15 | E-GEOD-44402 | biostudies-arrayexpress

RNAseq of PURA knockdown in HeLa cells

Project description:RNAseq of PURA knockdown in HeLa cells

| PRJNA798378 | ENA

Genomewide analysis of QKI-dependent alternative splicing

Project description:To identify QKI targets, we performed QKI knockdown in BEAS2B cells and analyzed alternative splicing patterns by high-throughput RNA sequencing. The mRNA profiles of control- and QKI-knockdown BEAS2B cells were generated by deep sequencing using Illumina GAIIx sequencer.

2014-04-14 | E-GEOD-55215 | biostudies-arrayexpress

The RNA helicase DDX39B regulates IL7R alternative splicing reducing the risk of Multiple Sclerosis

Project description:Purpose: The goal of this study is to investigate the role of DDX39B in RNA splicing Methods: RNA-Seq splicing analysis of HeLa cells with experimentally induced DDX39B expression knockdown

2017-03-28 | GSE94730 | GEO

Genomewide analysis of EGF-induced alternative splicing

Project description:We performed EGF treatment and hnRNP A1 knockdown in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing.

2017-03-01 | GSE92939 | GEO

RNA-seq analysis of alternative splicing events in duplicated genes of Arabidopsis thaliana indicates considerable qualitative and quantitative divergence

Project description:Divergence of alternative splicing in duplicated genes is investigated Three replicates of RNA-seq for Arabidopsis first true leaf tissue

2014-09-30 | E-GEOD-57579 | biostudies-arrayexpress

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