CRISPR-TRAPSeq identifies the QKI RNA binding protein as important for astrocytic maturation and control of thalamocortical synapses (CLIP-Seq dataset)

We immunoprecipitated QK-6 from P21 mouse brains to identify which mRNAs QK-6 binds to in vivo. Overall design: P21 mouse brains were flash frozen, powderized and UV crosslinked prior to homogenization and QK-6 IP, or IgG control IP. mRNA bound to QK-6 was extracted after size selection on SDS-PAGE. Sequencing libraries were made from these samples as well as total crosslinked mRNA from homogenized brain (Input). After RNA-Seq, reads were aligned to mouse genome. Using QK-6 IP samples, candidate locations of binding (peaks) were discovered using the Piranha peak calling algorithm in a gene agnostic fashion. These candidate peaks were then tested for enrichment by statistically comparing read depth of QK-6 IP vs. control (Igg IP and Input) at each peak using EdgeR. Final data file was annotated with gene coordinate information for those peaks overlaping genes based on mm2.