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RNA-seq of endothelial cells from 28 hours post fertilization sf3b1 mutant and sibling zebrafish

ABSTRACT: The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 (Sf3b1) are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development.

ORGANISM(S): Danio rerio

PROVIDER: GSE206017 | GEO | 2022/12/13

REPOSITORIES: GEO

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RNA-seq of endothelial cells from 28 hours post fertilization sf3b1 mutant and sibling zebrafish with Stat3 overexpression

Project description:The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 (Sf3b1). Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development.

2022-12-13 | GSE206019 | GEO

RNA-seq of erythroid cells from 24 hours post fertilization sf3b1 mutant and sibling zebrafish

Project description:The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development.

2019-05-01 | GSE129952 | GEO

RNA-seq of erythroid cells from 40 hours post fertilization ddx41 mutant and sibling zebrafish

Project description:The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead-box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development.

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RNA-seq of hematopoietic stem and progenitor cells from 40 hours post fertilization ddx41 mutant and sibling zebrafish

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Differential gene expression and exon usage in bone marrow from RARS patients with SF3B1 somatic mutations compared to healthy patients.

Project description:SF3B1, splicing factor 3b subunit 1 is a component of the RNA splicing machinery and it has been found to be highly mutated in refractory anemia with ring sideroblasts (RARS) and RARS associated with thrombocytosis (RARS-T). The aim of this study is to investigate the RNA splicing patterns in bone marrow from patients with SF3B1 somatic mutations compared to normal physiologic splicing. We compared the RNA splicing pattern as exon usage, differential gene expression, and pathway analysis with normal splicing mRNA profiles, as measured by RNA-Seq, in bone marrow derived mononuclear cells from 2 RARS patients with SF3B1 somatic mutations were compared to the mRNA profile of a normal donor.

2013-01-18 | E-GEOD-43603 | biostudies-arrayexpress

SF3B1 association with chromatin determines splicing outcomes

Project description:Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. Part of the explanation probably lies in differences in chromatin organization between exons and introns. Proteomic, co-immunoprecipitation, and sedimentation analyses described here indicated that SF3B1, an essential splicing component of the U2 snRNP complex, is strongly associated with nucleosomes. ChIP-seq and RNA-seq analyses revealed that SF3B1 is specifically bound to nucleosomes located at exonic positions. SF3B1 binding is enriched at nucleosomes positioned over short exons flanked by long introns that are also characterized by differential GC content between exons and introns. Disruption of SF3B1 binding to such nucleosomes affected the splicing of these exons similarly to inhibition of SF3B1 expression. Our findings suggest that the association of SF3B1 with nucleosomes is functionally important for splice site recognition and that SF3B1 conveys splicing-relevant information embedded in chromatin structure. MNase-seq on Input and SF3B1 pull-down, mRNA-seq on control and SF3B1 si-RNA treated cells as well as on TSA (Trichostatin A) treated and untreated cells.

2015-04-22 | E-GEOD-65644 | biostudies-arrayexpress

SF3B1 Degron knockdown RNA-seq

Project description:Knockdown of mutant and/or wild-type SF3B1 in MEL202 cell line by Degron knock-in, followed by RNA-seq, to identify splicing events governed by mutant SF3B1. Control: parental MEL202 cell line. Experiments: mutant-SF3B1 knockdown; wildtype-SF3B1 knockdown; mutant SF3B1 knockout. Treatments: each of these four conditions plus and minus shld.

2015-03-11 | E-GEOD-66719 | biostudies-arrayexpress

RNA-seq of human K562 leukemia cells with or without a mutation in SF3B1 (splicing factor 3b, subunit 1) that were treated with DMSO or the STAT3 inhibitor STATTIC

Project description:The purpose of the experiment was to define the gene expression and splicing alterations occurring when human wildtype or splicing factor 3b subunit 1 (SF3B1) mutant K562 cells had STAT3 inhibited with the small molecule STATTIC. Results provide insight the interplay of SF3B1 and STAT3 in human hematopoietic cells.

2022-12-13 | GSE206020 | GEO

Differential gene expression and exon usage in bone marrow from RARS patients with SF3B1 somatic mutations compared to healthy patients.

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Transcriptome analysis of SF3B1-mutation induced changes in K562 cells

Project description:Using RNA-Seq, we determined changes to gene expression and splicing on inducible expression of SF3B1-WT and SF3B1-MUT (K700E) in K562 cells. Using RNA-Seq, we determined changes to gene expression and splicing on inducible expression of SF3B1-WT and SF3B1-MUT (K700E) in K562 cells.

2016-07-15 | E-GEOD-70959 | biostudies-arrayexpress

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