Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

43 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SRp20 regulates Genome-wide Alternative RNA splicing events in U2OS cells

ABSTRACT: To examine the effects of SRp20 on genome-wide RNA splicing in tumor cells, we utilized Exonhit SpliceArray to compare genome-wide changes of RNA splicing and transcription in U2OS cells with or without knockdown of SRp20 by RNAi. U2OS cells were treated by SRp20 siRNA or non-specific siRNA, each performed in triplicate. A human genome-wide splice-array assay was performed by using a service provider ExonHit Therapeutics, Inc (Gaithersburg, MD). Fifty ng of total RNA isolated from U2OS cells with or without knockdown of SRp20 was quality controlled and analyzed by using Affymetrix GeneChip platform to profile the expression of 20,649 genes and splicing events of 19,066 genes.

ORGANISM(S): Homo sapiens

SUBMITTER: Zhi-Ming Zheng

PROVIDER: E-GEOD-22149 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

SRp20 regulates Genome-wide Alternative RNA splicing events in MEF3T3 cells

Project description:To examine the effects of SRp20 on genome-wide RNA splicing in mouse cells, we utilized Exonhit SpliceArrayTM to compare genome-wide changes of RNA splicing and transcription in MEF3T3 mouse fibroblasts with or without ectopic expression of SRp20. MEF3T3 tet-off cells were transfected with pRevTRE/T7-SRSF3 expression vector (pJR17) or pFLAG-CMV5.1 empty vector, each performed in triplicate. A mouse genome-wide splice-array assay was performed by using a service provider ExonHit Therapeutics, Inc (Gaithersburg, MD). Fifty ng of total RNA isolated from MEF3T3 cells with or without SRp20 overexpression was quality controlled and analyzed by using Affymetrix GeneChip platform.

2014-08-08 | E-GEOD-60147 | biostudies-arrayexpress

SRp20 regulates Genome-wide Alternative RNA splicing events in U2OS cells

Project description:To examine the effects of SRp20 on genome-wide RNA splicing in tumor cells, we utilized Exonhit SpliceArray to compare genome-wide changes of RNA splicing and transcription in U2OS cells with or without knockdown of SRp20 by RNAi.

2012-12-30 | GSE22149 | GEO

SRp20 regulates Genome-wide Alternative RNA splicing events in MEF3T3 cells

2014-08-08 | GSE60147 | GEO

Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors

Project description:Topoisomerase I (Top1) relaxes both positive and negative supercoilings by producing transient Top1 cleavage complexes (Top1cc). Several studies have suggested the implication of Top1 in splicing. Here, we tested the implication of Top1cc in splicing at the global genome level in human carcinoma cells to determine whether Top1 inhibition selectively affects particular families of genes. We tested the impact of Top1 inhibition on splicing at the genome-wide level in human colon carcinoma HCT116 cells. The RNA of HCT116 cells treated with camptothecin (CPT) for various times was analyzed with ExonHit Human Splice Array.

2011-07-21 | E-GEOD-23677 | biostudies-arrayexpress

Homo sapiens

Project description:SRp20 regulates Genome-wide Alternative RNA splicing events in U2OS cells

| PRJNA127707 | ENA

A splice isoform signature of ParkinsonM-bM-^@M-^Ys disease in peripheral blood

Project description:In these studies, we used splice variant-specific microarrays manufactured by the ExonHit company ( www.exonhit.com) on the Affymetrix platform. The goal was to identify splice isoforms whose expression is altered in whole blood of early-stage ParkinsonM-bM-^@M-^Ys disease patients compared to healthy and neurodegenerative disease controls. The study included 19 cases of ParkinsonM-bM-^@M-^Ys disease (PD) samples, 4 of multiple system atrophy (MSA), 4 progressive supranuclear palsy (PSP) and 10 healthy controls. Thirteen splice variants were confirmed in quantitative polymerase chain reactions and used to classify blinded samples from ParkinsonM-bM-^@M-^Ys disease patients and controls with 90% accuracy and 94% sensitivity. In these studies, we used splice variant-specific microarrays manufactured by the ExonHit company ( www.exonhit.com) on the Affymetrix platform. The study included 19 cases of ParkinsonM-bM-^@M-^Ys disease (PD) samples and 20 control samples including 4 cases of multiple system atrophy (MSA), 4 progressive supranuclear palsy (PSP) and 12 healthy controls. Splice isoforms differentially expressed in PD vs any other control group were identified and validated using real-time quantitative PCR on two independent sets of 33 coded and 53 blinded samples.

2012-12-01 | E-GEOD-34287 | biostudies-arrayexpress

RIP-chip by array of mouse undifferentiated and neural cells to identify mRNAs associated with SRp20 and SRp75

Project description:Members of the SR protein family of RNA binding proteins play numerous roles in gene expression, including the regulation of pre-mRNA splicing, mRNA export, and translation. How SR proteins coordinate gene expression programs is unknown, and comprehensive knowledge of endogenous mRNA targets is lacking. We established physiological expression of GFP-tagged SR protein, allowing the immunopurification and systematic identification of mRNAs associated with SRp20 and SRp75. This genome-wide analysis showed that SRp20 and SRp75 are components of distinct, mostly non-overlapping mRNPs in undifferentiated and neural cells.

2010-07-20 | E-MEXP-2637 | biostudies-arrayexpress

RNAi profiling by array of mouse P19 cells to investigate how SR proteins coordinate gene expression programs

Project description:Members of the SR protein family of RNA binding proteins play numerous roles in gene expression, including the regulation of pre-mRNA splicing, mRNA export, and translation. How SR proteins coordinate gene expression programs has been largely unexplored, and comprehensive knowledge of endogenous mRNA targets is lacking. Gene expression changes upon SRp20 or SRp75 RNAi in P19 parental, SRp75-BAC, and SRp20-BAC cells were measured with mouse whole genome microarrays. The knockdown of either SRp20 or SRp75 led to up- or downregulation of specific transcripts. Phenotypic rescue in the SRp75-BAC, and SRp20-BAC cells demonstrated functionality of the GFP-tagged SR proteins, and showed the specificity of the knockdowns.

2010-07-20 | E-MEXP-2640 | biostudies-arrayexpress

Mus musculus

Project description:SRp20 regulates Genome-wide Alternative RNA splicing events in MEF3T3 cells

| PRJNA257714 | ENA

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins

Project description:This SuperSeries is composed of the following subset Series: GSE34992: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splice array) GSE34993: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq) GSE34995: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq) Refer to individual Series

2012-02-20 | E-GEOD-34996 | 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