Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide Identification of RNA Bound by IGF2BP3 in Mouse Testes by eCLIP-seq

ABSTRACT: Transcriptome-wide Identification of RNA Bound by IGF2BP3 in Mouse Testes by eCLIP-seq

PROVIDER: PRJNA1077949 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30989833_1.fastq.gz	Fastqsanger.gz
	SRR30989833_2.fastq.gz	Fastqsanger.gz
	SRR30989834_1.fastq.gz	Fastqsanger.gz
	SRR30989834_2.fastq.gz	Fastqsanger.gz
	SRR30989835_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Transcriptome-wide Identification of RNA Bound by IGF2BP3 in Mouse Testes by eCLIP-seq

Project description:The knockout of IGF2BP3 affects the proper progress of spermatogenesis. We use Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) to find the targets bound by IGF2BP3 in the testis. After conducting joint analysis with the RNC-seq of knockout mice, we identified that changes in the downstream target genes of IGF2BP3 at the transcriptional and translational levels will damage the conversion of histones to protamines.

2025-02-05 | GSE256053 | GEO

NKAPL RNA targets in mouse testes with eCLIP-seq

Project description:To profile RNA targets of NKAPL on chromatin, we performed eCLIP-seq (enhanced crosslinking immunoprecipitation coupled with sequencing) using 21d wild-type mouse testes.

2024-12-12 | GSE232416 | GEO

NKAPL RNA targets in mouse testes with eCLIP-seq

Project description:NKAPL RNA targets in mouse testes with eCLIP-seq

| PRJNA971950 | ENA

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

Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [eCLIP-Seq]

Project description:Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using a recently developed enhanced UV crosslinking and immunoprecipitation (eCLIP) approach, we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad region- and binding site-level IMP1 and IMP2 show reproducible binding to a large and overlapping set of 3'UTR-enriched targets. RNA Bind-N-Seq applied to recombinant full-length IMP1 and IMP2 reveals CA-rich motifs that are enriched in eCLIP-defined binding sites. We observe that IMP1 loss in hPSCs recapitulates IMP1 phenotypes, including a reduction in cell adhesion and an increase in cell death. For cell adhesion, in hPSCs we find IMP1 maintains levels of integrin mRNA, specifically regulating RNA stability of ITGB5. Additionally, we show IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles. eCLIP-seq was performed in biological replicate for IGF2BP1/IMP1 and IGF2BP2/IMP2, as well as one replicate each for IGF2BP3/IMP3, RBFOX2, and an IgG control. Each sample has a size-matched input control for analysis

2016-04-07 | E-GEOD-78507 | biostudies-arrayexpress

The RNA binding protein IGF2BP3 is required MLL-AF4 mediated leukemogenesis

Project description:In our study, we found that MLL-AF4 transcriptionally induces IGF2BP3 and is required for MLL-Af4 mediated leukemogenesis. Deletion of murine Igf2bp3 significantly increased the survival of mice with MLL-Af4 driven leukemia and greatly attenuated disease. Furthermore, Igf2bp3 was necessary for the development of and the self-renewal capacity of MLL-Af4 leukemic initiating cells. eCLIP and transcriptome analysis of MLL-Af4 transformed stem and progenitor cells and primary cells from MLL-Af4 leukemic mice revealed an IGF2BP3-regulated post-transcriptional operon governing tumor cell survival and proliferation. Critical mRNA targets include the Hoxa locus and numerous genes within the Ras signaling pathway. Together, our findings show that IGF2BP3 is an essential positive regulator of MLL-AF4 mediated leukemogenesis and is a potential therapeutic target in this disease.

2021-08-11 | GSE156115 | GEO

eCLIP from HepG2 (ENCSR993OLA)

Project description:eCLIP experiment on HepG2 against IGF2BP3 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2017-01-04 | GSE92220 | GEO

eCLIP from HepG2 (ENCSR077KVG)

Project description:eCLIP control experiment on HepG2 against IGF2BP3 For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2017-01-03 | GSE91453 | GEO

RNA immunoprecipitation (RIP) of IGF2BP3 from pancreatic cancer cell extracts cultured on fibronectin

Project description:IGF2BP3-bound transcripts were identified by RNA immunoprecipitation and sequencing (RIP-Seq) and bioinformatics analysis. A pancreatic cancer cell line S2-013 was cultured on fibronectin. We performed RIP of IGF2BP3 using anti-IGF2BP3 antibody from the fibronectin-stimulated S2-013 extracts, and identified the associated mRNAs using a next generation sequencer.

2016-11-09 | GSE47597 | GEO

IGF2BP3 controls cancer cell invasiveness by modulation RISC function

Project description:The goal of this study was to determine IGF2BP3 regulation of RNA targets in human pacreatic ductal adenocarcinoma cell lines Included are iCLIP-seq libraries for IGF2BP3 from PL45 and Panc1 PDAC cell samples, RIP-seq samples from PL45 and Panc1 PDAC cells, RNA-seq data sets from control and IGF2BP3 knockdown in PL45 and Panc1 PDAC cells, and small RNA-seq samples from Panc1 cells

2016-03-12 | E-GEOD-79147 | biostudies-arrayexpress

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