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Mus musculus

ABSTRACT: NOVA2 and NOVA1 HITS-CLIP in wild-type mouse cortex (E18.5)

PROVIDER: PRJNA286234 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3532940.fastq.gz	Fastqsanger.gz
	SRR3532941.fastq.gz	Fastqsanger.gz
	SRR3532942.fastq.gz	Fastqsanger.gz
	SRR3532943.fastq.gz	Fastqsanger.gz
	SRR3532944.fastq.gz	Fastqsanger.gz

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NOVA2 and NOVA1 HITS-CLIP in wild-type mouse cortex (E18.5)

Project description:Mouse cortex samples from E18.5 wild-type were subjected to HITS-CLIP to detect NOVA2 and NOVA1 binding positions on RNA

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RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain

Project description:We sequenced mRNA from E18.5 mouse cortex (3 wild-type vs 3 Nova2-/- and 3 wild-type vs 3 Nova1-/-) and from E18.5 mouse mid- and hind-brain (3 wild-type vs 3 Nova1-/-) to compare gene expression level and alternative splicing events between wild-type and Nova mutant mice.

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NOVA2 cTag-CLIP

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.

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NOVA1 HITS-CLIP in wild-type mouse diencephalon/ mesencephalon (P21)

Project description:Mouse diencephalon/ mesencephalon samples from P21 wild-type were subjected to HITS-CLIP to detect NOVA1 binding positions on RNA

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Wild type vs. Nova2 KO mouse P10 cortex RNA

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

Mus musculus

Project description:RNAseq in E18.5 wild-type, Nova2-KO, and Nova1-KO mouse cortex and mid- and hind-brain

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NOVA1 HITS-CLIP in wild-type mouse diencephalon/ mesencephalon (P21)

Project description:NOVA1 HITS-CLIP in wild-type mouse diencephalon/ mesencephalon (P21)

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Wild type vs. Nova2 KO mouse E14.5 cortex RNA

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

Mus musculus

Project description:Wild type vs. Nova2 KO mouse E14.5 cortex RNA

| PRJNA128269 | ENA

Wild type vs. Nova2 KO mouse: Exon junction array data

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 | GSE17376 | GEO

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