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Mus musculus strain:CD1

ABSTRACT: Rbfox target network (HITS-CLIP in mouse brain)

PROVIDER: PRJNA234443 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1107530.fastq.gz	Fastqsanger.gz
	SRR1107540.fastq.gz	Fastqsanger.gz
	SRR1107531.fastq.gz	Fastqsanger.gz
	SRR1107532.fastq.gz	Fastqsanger.gz
	SRR1107533.fastq.gz	Fastqsanger.gz

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Project description:To estimate transcripts levels in P13 mouse neocortex. MicroRNAs (miRNAs) play critical roles in the regulation of gene expression. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. We used HITS-CLIP to covalently crosslink native Argonaute (Ago) protein-RNA complexes in mouse brain. This produced two simultaneous datasets—Ago-miRNA and Ago-mRNA binding sites—that were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Here we include the expression data obtained from dissected P13 mouse neocortex. These data are used for in silico CLIP simulation for normalization of Ago HITS-CLIP tags and also for selecting transcripts expressed in P13 mouse cortex.

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Mus musculus

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

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Mus musculus

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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

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