NOVA2 cTag-CLIP and Nova2-cKO RNA-seq in mouse brain
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA400798 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5991050.fastq.gz | Fastqsanger.gz | |||
| SRR5991060.fastq.gz | Fastqsanger.gz | |||
| SRR5991070_1.fastq.gz | Fastqsanger.gz | |||
| SRR5991070_2.fastq.gz | Fastqsanger.gz | |||
| SRR5991080_1.fastq.gz | Fastqsanger.gz |
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Project description:Mouse cortex or cerebellum samples from E18.5 or P28 Nova2-cTag mouse crossed with a series of Cre driver mice were subjected to Nova2 cTag-CLIP to generate functional NOVA2-RNA maps from single neuronal populations in the mouse brain.
2019-01-09 | GSE103315 | 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:We sequenced RNA from adult mouse spinal cord and from cell sorted Nova2-cKO neurons (crossed with Emx1-Cre, Gad2-Cre, Pcp2-Cre driver mice) and from Nova2.Ptbp2-dKO to compare gene expression level, and alternative splicing events.
2019-01-09 | GSE103314 | GEO
Project description:Msi1_HITS-CLIP in E14.5 mouse brain
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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: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: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:IMP2/IGF2BP2 HITS-CLIP from E13.5 mouse brain
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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.
2009-11-04 | GSE17374 | GEO
Project description:To assess the requirement of Nova2 for alternative processing of RNA in the developping brain. Neuronal migration leads to a highly organized laminar structure in the mammalian brain and its mis-regulation causes lissencephaly, behavioral and cognitive defects. Reelin signaling, mediated in part by a key adaptor, disabled-1 (Dab1), plays a critical but incompletely understood role in this process. We found that the neuron-specific RNA binding protein Nova2 regulates neuronal migration in late-generated cortical and Purkinje neurons. An unbiased HITS-CLIP and exon junction array search for Nova-dependent RNAs at E14.5 focused on components of the reelin pathway revealed only one candidate—an alternatively spliced isoform of Dab1 (Dab1.7bc). In utero electroporation demonstrated that Dab1.7bc was sufficient to induce neuronal migration defects in wild-type mice and exacerbate defects when Dab1 levels were reduced, while Dab1 overexpression mitigates defects in Nova2-null mice. Thus Nova2 regulates an RNA switch controlling the ability of Dab1 to mediate neuronal responsiveness to reelin signaling and neuronal migration, suggesting new links between splicing regulation, brain disease and development. Keywords: Comparative analysis RNA from the cortex of 3 wild type and 3 Nova2 KO E14.5 cortex. One array per biological replicate.
2010-07-07 | E-GEOD-22758 | biostudies-arrayexpress