Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spliceosome iCLIP in multiple cell lines

ABSTRACT: Spliceosome iCLIP in multiple cell lines

PROVIDER: PRJEB33667 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3450310.fastq.gz	Fastqsanger.gz
	ERR3450320.fastq.gz	Fastqsanger.gz
	ERR3450330.fastq.gz	Fastqsanger.gz
	ERR3450340.fastq.gz	Fastqsanger.gz
	ERR3450311.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 40

Similar Datasets

Spliceosome iCLIP in multiple cell lines

Project description:The studies of spliceosomal interactions are challenging due to their dynamic nature. Here we developed spliceosome iCLIP, which immunoprecipitates SmB along with snRNPs and auxiliary RNA binding proteins (RBPs) to simultaneously map the spliceosomal binding to human snRNAs and pre-mRNAs. This identified 9 distinct regions on pre-mRNAs, which overlap with position-dependent binding patterns of 15 RBPs. Using spliceosome iCLIP, we additionally identified >50,000 branchpoints (BPs) that have canonical features, unlike those identified by RNA-seq. The iCLIP BPs generally overlap with the computationally predicted BPs, and alternative BPs are associated with extended regions of structurally accessible RNA. We find that the position and strength of BPs defines the binding patterns of SF3 and U2AF complexes, whereas the RNA structure around BPs affects the sensitivity of exons to perturbation of these complexes. Our findings introduce spliceosome iCLIP as a new method for transcriptomic studies of BPs and splicing mechanisms.

2019-08-03 | E-MTAB-8182 | biostudies-arrayexpress

Spliceosome iCLIP

Project description:Spliceosome iCLIP

| PRJEB27592 | ENA

Spliceosome iCLIP

2019-08-30 | E-MTAB-6950 | biostudies-arrayexpress

LARP iCLIP in MDAMB231 cell lines

Project description:LARP iCLIP in MDAMB231 cell lines

| PRJEB40636 | ENA

LARP iCLIP in MDAMB231 cell lines

Project description:This experiment aims to globally identify LARP6 binding sites on the transcriptome by performing iCLIP in MDA-MB231 cell lines expressing GFP-LARP6. MDA-MB231 cell lines expressing GFP only were used as controls in the experiment.

2020-11-01 | E-MTAB-9636 | biostudies-arrayexpress

Transcriptomic analysis of multiple myeloma cell lines

Project description:Transcriptomic analysis of multiple myeloma cell lines

| PRJNA433025 | ENA

Cohesin ChIP-seq in multiple cell lines

Project description:Cohesin ChIP-seq in multiple cell lines

| PRJNA849415 | ENA

iCLIP-Seq analyses of DDX46-bound RNAs

Project description:DDX46 is identified to be required at the early step of pre-spliceosome assembly,but the potential roles of DDX46 in RNA editing and whether DDX46 could regulate antiviral innate immunity by editing antiviral transcripts in the nucleus remain elusive. iCLIP-Seq analyses of DDX46-bound RNAs from uninfected and VSV-infected RAW264.7 cells

2016-05-13 | E-GEOD-81386 | biostudies-arrayexpress

Ro60 iCLIP

Project description:Autoantibodies target the RNA-binding protein Ro60 in systemic lupus erythematosus (SLE) and Sjögren's syndrome. However, whether Ro60 and its associated RNAs contribute to disease pathogenesis is unclear. We catalogued the Ro60-associated RNAs in human cell lines. iCLIP in 2 cell lines (GM12878, K562).

2015-09-16 | E-GEOD-72500 | biostudies-arrayexpress

Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma

Project description:Resistance to proteasome inhibitors (PIs) is a ubiquitous clinical concern in multiple myeloma (MM). We proposed that signaling-level responses after PI would reveal new means to enhance efficacy. Unbiased phosphoproteomics after the PI carfilzomib surprisingly demonstrated the most prominent phosphorylation changes on spliceosome components. Spliceosome modulation was invisible to RNA or protein abundance alone. Transcriptome analysis demonstrated broad-scale intron retention suggestive of PI-specific splicing interference. Direct spliceosome inhibition synergized with carfilzomib and showed potent anti-myeloma activity. Functional genomics and exome sequencing further supported the spliceosome as a specific vulnerabilityin myeloma. Our results propose splicing interference as an unrecognized modality of PI mechanism, reveal additional modes of spliceosome modulation, and suggest spliceosome targeting as a promising therapeutic strategy in myeloma.

2020-02-18 | GSE124510 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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