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Next Generation Sequencing Analysis of Wild Type and SRSF10-/- embryonic day 13.5 heart Transcriptomes

ABSTRACT: We generated the SRSF10 -/- mice, and collected their embryonic heart at 13.5 and controls. Then, we extracted RNAs of embryonic heart and performed next generation sequencing. By comparing sequcing data from WT and SRSF10 -/- samples, we profiled the alternative splicing events and gene expression regulated by SRSF10 during mouse heart development process.

ORGANISM(S): Mus musculus

PROVIDER: GSE66965 | GEO | 2015/04/01

SECONDARY ACCESSION(S): PRJNA278507

REPOSITORIES: GEO

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Next Generation Sequencing Analysis of Wild Type and SRSF10-/- embryonic day 13.5 heart Transcriptomes

Project description:We generated the SRSF10 -/- mice, and collected their embryonic heart at 13.5 and controls. Then, we extracted RNAs of embryonic heart and performed next generation sequencing. By comparing sequcing data from WT and SRSF10 -/- samples, we profiled the alternative splicing events and gene expression regulated by SRSF10 during mouse heart development process. E13.5 embryonic heart mRNA profiles of wild type (WT) and SRSF10-/- mice were generated by deep sequencing, using Illumina HiSeq2000.

2015-04-01 | E-GEOD-66965 | biostudies-arrayexpress

Nos1ap constitutive null mice embryonic day 13.5 heart transcriptome

Project description:To assess the impact of Nos1ap loss on heart transcriptome during development, RNA-seq was performed in heart tissue from wildtype (males; n=5) and Nos1ap null homozygous (males; n=5) embryonic day 13.5 (e13.5) mice, and assessed for differential gene expression. At a false discovery rate of 1% and an absolute log2-fold change over 1, only two genes (Mt2 and Gm7694) were differentially expressed. These findings indicate that constitutive loss of Nos1ap has no major widespread impact on transcriptome in e13.5 hearts.

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SRSF10 regulates alternative splicing and is required for adipocyte differentiation.

Project description:During adipocyte differentiation, significant alternative splicing changes occur in association with the adipogenic process. However, little is known about roles played by splicing factors in this process. We observed that mice deficient for the splicing factor SRSF10 exhibit severely impaired development of subcutaneous white adipose tissue as a result of defects in adipogenic differentiation. To identify splicing events responsible for this, RNA-seq analysis was performed using embryonic fibroblast cells. Several SRSF10-affected splicing events that are implicated in adipogenesis have been identified. Skipping of lipin1 exon 7 is controlled by SRSF10-regulated cis-element located in the constitutive exon 8. The activity of this element depends on the binding of SRSF10 and correlates with the relative abundance of lipin1a mRNA. A series of experiments demonstrated that SRSF10 controls the production of lipin1a and thus promotes adipocyte differentiation. Indeed, lipin1a expression could rescue SRSF10-mediated adipogenic defects. Taken together, our results identify SRSF10 as an essential regulator for adipocyte differentiation and also provide new insights into splicing control by SRSF10 in lipin1 pre-mRNA splicing. RNA-seq for wide type (WT) and SRSF10-deficient (KO) mouse MEF cells

2014-05-12 | E-GEOD-54226 | biostudies-arrayexpress

SRSF10 regulates alternative splicing and is required for adipocyte differentiation.

2014-05-12 | GSE54226 | GEO

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

Mus musculus

Project description:Next Generation Sequencing Analysis of Wild Type and SRSF10-/- embryonic day 13.5 heart Transcriptomes

| PRJNA278507 | ENA

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

2014-01-22 | GSE53354 | GEO

WGBS from heart (ENCSR149GUT)

Project description:Whole genome bisulfite-seq on embryonic 13.5 day mouse heart For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-06-22 | GSE82469 | GEO

microRNA-seq from heart (ENCSR329THX)

Project description:miRNA-seq on embryonic 13.5 day mouse heart For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-06-22 | GSE82604 | GEO

ChIP-seq from heart (ENCSR098USP)

Project description:H3K9me3 ChIP-seq on embryonic 13.5 day mouse heart For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-06-22 | GSE82431 | GEO

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