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GenomicsSF3B1 association with chromatin determines splicing outcomes
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. Pro...
ORGANISM(S): Homo sapiens 
2015-04-22 | E-GEOD-65644 | biostudies-arrayexpress
TranscriptomicsRNA sequencing of bone marrow CD34+ cells from myelodysplastic syndrome patients with and without SF3B1 mutation and from healthy controls
The splicing factor SF3B1 is the most commonly mutated gene in the myelodysplastic syndromes (MDS), particularly in patients with refractory anemia with ring sideroblasts (RARS). MDS is a disorder of the hematopoietic stem cell and we thus studied the transcriptome of CD34+ cells from MDS patients w...
ORGANISM(S): Homo sapiens 
2014-11-22 | E-GEOD-63569 | biostudies-arrayexpress
TranscriptomicsTranscriptomic analyses of primary uveal melanomas
SF3B1 is coding an essential splicing factor. This gene was found recurrently mutated in uveal melanoma. To understand the consequences of these hotspot SF3B1 mutations, we performed high coverage RNA-seq on 74 primary uveal melanomas, which were treated by primary enucleation. We analyzed data for...
ORGANISM(S): Homo sapiens 
2016-07-03 | E-MTAB-4097 | biostudies-arrayexpress
TranscriptomicsTranscriptome analysis of chronic lymphoid leukemia reveals isoform regulation associated with mutations in SF3B1
Several DNA sequencing studies of chronic lymphocytic leukemia (CLL) revealed that the splicing factor SF3B1 accumulated somatic point mutations in about 10 percent of the patients. In most cases the mutations were located in the genomic regions coding for the C-terminal HEAT-repeat domain and in ma...
ORGANISM(S): Homo sapiens 
2013-12-27 | E-MTAB-2025 | biostudies-arrayexpress
TranscriptomicsSF3B1 Degron knockdown RNA-seq
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 ...
ORGANISM(S): Homo sapiens 
2015-03-11 | E-GEOD-66719 | biostudies-arrayexpress
ProteomicsDetermination of Trunk Neural Crest Cell Fate and Susceptibility to Splicing Perturbation by the DLC1-SF3B1-PHF5A splicing complex
How the ubiquitously expressed splicing factors specifically regulate neural crest (NC) development and enhance their vulnerability to splicing perturbations remain poorly understood. Here, we show that NC-specific DLC1, partnering with SF3B1-PHF5A splicing complex, are crucial for determining avian...
ORGANISM(S): Gallus Gallus 
PXD064804 |
TranscriptomicsTranscriptome analysis of SF3B1-mutation induced changes 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. Using RNA-Seq, we determined changes to gene expression and splicing on inducible expression of SF3B1-WT and SF3B1-MUT (K700E) in K562 cells.
ORGANISM(S): Homo sapiens 
2016-07-15 | E-GEOD-70959 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of human K-562 leukaemia cell line with and without K700E mutation in coding region of SF3B1 gene
The aim of this experiment was to compare the transcriptomes of SF3B1 mutant and wildtype isogenic cells at the whole cell, nuclear and cytoplasmic levels. Mutations in SF3B1 are often found in the malignant cells of patients suffering from myelodysplastic syndromes and more rarely in other cancer t...
ORGANISM(S): Homo sapiens 
2019-02-25 | E-MTAB-7192 | biostudies-arrayexpress
ProteomicsConsequences of SF3B1 mutation on the proteome
In this study, we evaluated the differential proteome of SF3B1-mutated and SF3B1-Wild-Type uveal melanoma cells (isogenic Mel202 cells). We performed a quantitative label-free tandem liquid chromatography mass spectrometry (LC-MS/MS) analysis of SF3B1WT and SF3B1mut Mel202 cells.
ORGANISM(S): Homo sapiens (Human) 
2022-03-15 | PXD022726 | Pride
Cancer Uveal melanoma Sf3b1 Proteome Mutation 
ProteomicsCharacterization of the SF3B1 interactome
CDK9 is a critical kinase required for the productive transcription of protein-coding genes by RNA polymerase II (pol II). As part of P-TEFb, CDK9 phosphorylates the carboxyl-terminal domain (CTD) of pol II and elongation factors, including SPT5, which allows pol II to elongate past the early elonga...
ORGANISM(S): Homo sapiens (Human) 
2022-08-22 | PXD033694 | Pride
Transcription Splicing Sf3b1 Interactome 
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