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SR protein family in P19 cells

ABSTRACT: SR protein family in P19 cells

PROVIDER: PRJNA286285 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2057570.fastq.gz	Fastqsanger.gz
	SRR2057580.fastq.gz	Fastqsanger.gz
	SRR2057590.fastq.gz	Fastqsanger.gz
	SRR2058230.fastq.gz	Fastqsanger.gz
	SRR2058240.fastq.gz	Fastqsanger.gz

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Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

2016-03-07 | GSE69733 | GEO

Knockdown of SR protein family in P19 cells and RNA-seq of cytoplasmic and whole cell polyA+ RNA

Project description:Our data suggest that all SR proteins contribute to mRNA export via NXF1. To identify endogenous export targets we depleted all seven SR proteins individually from P19 WT cells prepared cytoplasmic fractions. We sequenced the cytoplasmic fraction and as a control whole celll RNA from the identical sample. Knockdown of seven SR Proteins plus control, total RNA and cytoplasmic RNA, polyA+ enriched, 2 biological replicates per condition, 2 technical replicates per condition

2016-03-07 | E-GEOD-69733 | 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

RNA-seq analysis of the eight Drosophila SR protein family members

Project description:Using RNA-seq, we characterize the global AS regulation of the eight Drosophila SR protein family members RNA-seq experiments on two replicate samples from 8 individual SR protein knockdown (exptGroup=S), two replicates of simultaneous SR protein knockdown (XL6:B52 & SC35:B52) (exptGroup=D). Each exptGroup includes duplicate of its own non-specific (NS) controls.

2014-11-23 | E-GEOD-63263 | biostudies-arrayexpress

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Project description:Using RNA-seq, we characterize the global AS regulation of the eight Drosophila SR protein family members

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Transcriptome-wide mapping of RNA:protein interactions of seven SR proteins and NXF1 in P19 cells by iCLIP

Project description:We used GFP-tagged SR proteins expressed at endogenous levels and iCLIP to identify and compare endogenous RNA targets of individual SR proteins, map the preferential sites of binding, compare binding pattern and binding motifs between family members and to NXF1 and quantify binding of SR proteins and NXF1 to spliced versus unspliced RNAs to study the role of SR proteins in mRNA export via NXF1.

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SR protein family in P19 cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-03-07 | GSE69734 | GEO

A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast

Project description:Mammalian SR proteins are a family of reversibly phosphorylated RNA binding proteins primarily studied for their roles in alternative splicing. While budding yeast lack alternative splicing, they do have three SR-like proteins: Npl3, Gbp2, and Hrb1. However, these have been primarily studied for their roles in mRNA export, leaving their potential roles in splicing largely unexplored. Here we combined high-density genetic interaction profiling and genome-wide splicing-sensitive microarray analysis to demonstrate that a single SR-like protein, Npl3, is required for efficient splicing of a large set of pre-mRNAs in Saccharomyces cerevisiae. We tested the hypothesis that Npl3 promotes splicing by facilitating co-transcriptional recruitment of splicing factors. Using chromatin immunoprecipitation, we showed that mutation of NPL3 reduces the occupancy of U1 and U2 snRNPs at Npl3-stimulated genes. This provides the first evidence that an SR protein can promote recruitment of splicing factors to chromatin. Splicing-specific microarrays were used to assay changes to splicing in single and double deletion mutants of non-essential SR proteins, in a deletion mutant of a non-essential component of the nonsense-mediated decay pathway, and in a double deletion mutant of in an SR protein plus a non-sense mediated decay factor in Saccharomyces cerevisiae. The data includes both samples obtained at the permissive temperature and also shifts to the non-permissive temperature for some mutants, as well as dye-flipped technical replicates.

2008-12-30 | E-GEOD-11491 | biostudies-arrayexpress

p19-WT and p19-T111BpyAla treatment of extracted small RNAs

Project description:small RNA fractions were treated with either p19-WT or T111BpyAla to evaluate the catalytic ability of p19-T111BpyAla compared to the WT protein in degrading miRNAs

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A single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast

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