RNA-Seq of samples from mouse retina of Msi1/Msi2 double knockout in photoreceptor cells

The Musashi proteins, Msi1 and Msi2, are RNA binding proteins involved in control of mRNA translation and pre-mRNA splicing. This study characterizes the RNA expression and alternative splicing in the retina of Msi1/Msi2 double knockout mouse compared to floxed controls. The study is paired with quantitative proteomics of matching retinal samples (ProteomeXchange identifier PXD030748) and eCLIP-Seq mapping of MSI1 binding to retinal RNA (PRJNA795195). The Msi1 and Msi2 genes were knocked out in photoreceptor cells using tamoxifen inducible Cre (Cre-ERT2) under the control of Pde6g promoter. Tamoxifen was administered by intraperitoneal injection for three consecutive day starting at postnatal day 30, and the retina was collected at postnatal day 51. Retinas from floxed animals lacking the Cre recombinase and treated with tamoxifen were used as controls. Four biological replicates for each knockout and control group were used. rRNA subtracted libraries were prepared using KAPA Hyper RNA with Riboerase kit at the West Virginia University Genomics core. The libraries were sequenced at the University of Illinois DNA Services Lab on Illumina HiSeq4000 at average depth of 44 million paired 101 nt long reads per library.