Deep Sequencing of Cas9 editing and RNA splicing outcomes in mouse cells

We constructed a diverse genome-integrated library of splice acceptor sequences targeted by multiple SpCas9 guide RNAs in mouse embryonic stem cells. End-joining repair following Cas9 induced double stranded breaks may disrupt the genomic sequence of these splice sites sufficiently to cause skipping of their exons. We sequenced the genomic DNA to identify the guide RNA sequences, the primary transcripts to elucidate the Cas9 editing outcomes, and the spliced transcripts to measure exon skipping.