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

GSE17376 Mus musculus Genome binding/occupancy profiling by array 6 samples Submitted 2009/11/04 Platform GPL8940
Summary
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.
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Direct links to NCBI, no account and no request form: the whole study as GSE17376_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples.

Also filed as BioProject PRJNA119109. Searching any of these in the dataset finder brings you back here.

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