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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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22149 | GEO | 2012/12/30

SECONDARY ACCESSION(S): PRJNA127707

REPOSITORIES: GEO

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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. 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.

2012-12-30 | E-GEOD-22149 | biostudies-arrayexpress

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

2014-08-08 | GSE60147 | GEO

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

Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.

Project description:Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions. RNA-seq for wide type (WT) and SRSF10-deficient (KO) chicken DT40 cells

2014-01-22 | E-GEOD-53354 | biostudies-arrayexpress

Identification of alternative splicing events regulated by the splicing factor SRSF1 using data from exon-junction microarray technologies

Project description:Analysis to identify genome-wide differential alternative splicing events in A549 cells in which the levels of the gene SRSF1 were down-regulated with a specific siRNA

2013-12-18 | GSE53410 | GEO

Identification of alternative splicing events regulated by the splicing factor SRSF1 using data from exon-junction microarray technologies

Project description:Analysis to identify genome-wide differential alternative splicing events in A549 cells in which the levels of the gene SRSF1 were down-regulated with a specific siRNA 9 samples from three independent experiments using A549 cells transfected with lipofectamine alone, scramble siRNA or SRSF1 siRNA

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Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Project description:This SuperSeries is composed of the following subset Series: GSE23513: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY) GSE23514: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array) Refer to individual Series

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Determining the impact of alternative splicing events on transcriptome dynamics

Project description:Background The complete sequencing of the human genome and its subsequent analysis revealed a predominant role for alternative splicing in the generation of proteome diversity. Splice switching oligonucleotides (SSOs) are a powerful and specific tool to experimentally control alternative splicing of endogenous messenger RNAs in living cells. SSOs also have therapeutic potential to treat diseases that are caused by aberrant splicing. The assignment of biological roles to alternative splicing events of currently unknown function promises to provide a largely untapped source of potential new therapeutic targets. Here we have developed a protocol that combines high sensitivity microarrays with the transfection of SSOs to monitor global changes in gene expression downstream of alternate, endogenous splice events. Findings When applied to a well-characterized splicing event in the Bcl-x gene, the application of high sensitivity microarrays revealed a link between the induction of the Bcl-xS isoform and the repression of genes involved in protein synthesis. Conclusions The strategy introduced herein provides a useful approach to define the biological impact of any given alternative splicing event on global gene expression patterns. Furthermore, our data provide the first link between Bcl-xS expression and the repression of ribosomal protein gene expression. Biological triplicates, 2 conditions: control oligonucleotide, Bcl-x oligonucleotide

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Genome wide localizatoin of ORCA during G1 phase in U2OS cells and map of methyl-CpG sites in U2OS cells

Project description:ORCA is an ORC associated protein that plays important roles in replication initiation as well as heterochromatin organization. We carried out ORCA ChIP-seq in U2OS cells synchronized at different stage of G1 phase to determine its genome wide localization. To understand the genomic features of ORCA binding regions, we also carried out Methylated DNA IP (MeDIP) followed by deep sequencing in U2OS cells to determine the genome wide localizatoin of methyl-CpG sites in U2OS cells and how ORCA bidning regions co-localize with this important repressive mark.

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Determining the impact of alternative splicing events on transcriptome dynamics

2008-10-02 | GSE9851 | GEO