Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identifying SF3B1 binding sites across the transcriptome

ABSTRACT: Revealing the binding sites of endogenous SF3B1 using HITS-CLIP (high-throughput sequencing coupled with cross-linking immunoprecipitation).

ORGANISM(S): Homo sapiens

PROVIDER: GSE160948 | GEO | 2021/03/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identifying SNRPA1 binding sites across the transcriptome

Project description:Revealing the binding sites of endogenous SNRPA1 using irCLIP (cross-linking immunoprecipitation).

2021-03-30 | GSE160949 | GEO

Global analysis of binding sites of SF3B1 by CLIP-seq

Project description:SF3B1 is one of shared components of U2 and U12 snRNPs that are required for splicing of U2-type and U12-type introns, respectively. Interestingly, recurrent somatic mutations have been identified in the spliceosome components in human cancer. By using CLIP-seq for SF3B1, binding sites in human embryonic stem cells were determined. The most prominent binidng sites were at 3' splice sites on pre-mRNA. Interestingly, 5' and 3' ends of introns spliced out were enriched by CLIP.

2023-04-26 | GSE222867 | GEO

Identifying SF3B1 binding sites across the transcriptome

Project description:Identifying SF3B1 binding sites across the transcriptome

| PRJNA674891 | ENA

Argonaute HITS-CLIP in wild-type and APOBEC1-deficient BMDMs

Project description:To investigate the possible consequences of APOBEC1 editing for miRNA targeting, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) of the Argonaute (Ago) proteins (Chi et al., 2009) was performed in BMDMs derived from wild-type and Apobec1-/- littermates.

2017-11-21 | GSE58798 | GEO

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

Elucidation of Transcriptome-Wide MicroRNA Binding Sites in Human Cardiac Tissues by Ago2 HITS-CLIP

Project description:We deciphered Ago2:RNA interactions in post-mortem human heart tissues using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts.

2016-08-09 | GSE83410 | GEO

Genome-wide binding sites of RBM46 in mouse testes.

Project description:We carried out RBM46 eCLIP-seq (enhanced cross-linking immunoprecipitation coupled with sequencing) in wild-type testes and reported genome-wide occupancy of RBM46 in mouse testes.

2022-08-31 | GSE197280 | GEO

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

Elucidation of Transcriptome-Wide MicroRNA Binding Sites in Human Cardiac Tissues by Ago2 HITS-CLIP

2016-08-09 | E-GEOD-83410 | biostudies-arrayexpress

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Project description:UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are the most frequently used methods to study protein-RNA interactions in the intact cells and tissues, but their relative advantages or inherent biases have not been evaluated. To benchmark CLIP and iCLIP method, we performed iCLIP with Nova protein, which is the most extensively studied protein by CLIP. Further, we assessed UV-C-induced cross-linking preferences, by exploiting the UV-independent formation of covalent RNA cross-links of the mutant RNA methylase NSUN2.

2012-07-20 | E-MTAB-1008 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data