Nova HITS-CLIP and RNA-Seq in mouse cortex
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA286233 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mouse cortex samples from E18.5 wild-type were subjected to HITS-CLIP to detect NOVA2 and NOVA1 binding positions on RNA
2016-05-26 | GSE69710 | GEO
Project description:We report cell type specific Nova HITS-CLIP using BAC-transgenic lines expressing GFP-Nova under the motor neuron specific choline acetyltransferase (Chat) promoter. By comparing transcriptome wide Nova binding map in motor neurons and that in the whole spinal cord, we identified differential Nova binding sites in motor neurons, which correlate with motor neuron specific RNA processing.
2018-07-04 | GSE71294 | GEO
Project description:To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3â UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo. Keywords: Comparative analysis Refer to individual Series. This SuperSeries is composed of the following subset Series: GSE17374: Wild type vs. Nova2 KO mouse: Exon array data GSE17376: Wild type vs. Nova2 KO mouse: Exon junction array data
2010-06-20 | E-GEOD-12965 | biostudies-arrayexpress
Project description:To assess the requirement of Nova2 for alternative processing of RNA in mouse brain. Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3’ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo. This SuperSeries is composed of the SubSeries listed below.
2009-11-04 | GSE12965 | GEO
Project description:Mouse samples were subjected to HITS-CLIP to monitor Elavl binding
2019-09-30 | GSE104025 | GEO
Project description:HITS-CLIP is performed for the RNA-binding protein, IMP2/IGF2BP2, from E13.5 mouse brain.
2016-06-06 | E-MTAB-3636 | biostudies-arrayexpress
Project description:In order to identify YBX1 binding sites on endogenous RNA, we performed HITS-CLIP on endogenous YBX1 We used a previously published method to perform HITS-CLIP on endogenous YBX1 (Licatalosi D, et al. 2008, Nature 456:464-U22)
2015-05-08 | E-GEOD-63604 | biostudies-arrayexpress