Figure 5. Cell-type specific mRNA processing.

(a) Heat map showing the number of differentially processed exons (N = 567 out of 256,430 examined) for each pairwise comparison of transcriptomic cell types (Methods). (b–e) Confirmation of differential exon processing for four gene examples from (a) using MISO (Methods). Schematic of each gene (top) and corresponding quantitation (bottom).The MISO score (Ψ), or “percent spliced-in”, represents the relative exon usage of transcript variant b vs. a, for each gene in each cell type. The significance in pairwise comparisons for all cell types for each alternatively processed exon was measured by the Bayes factor (Bf); Bf > 100 is considered significant. Bf for each alternatively processed mRNA is presented as the heat map to the right; yellow represents strongest statistical significance of Bf = 10¹². (b) In agreement with a population-level transcriptome profiling study¹³, pyruvate kinase (Pkm) mRNAs display differential exon usage among neurons and non-neuronal cells. (c) Syntaxin binding protein 1 (Stxbp1) mRNAs show differential processing among broad neuronal types, but also specific Vip types. (d,e) mRNAs for AMPA receptor genes, Gria1 and Gria2, both display mutually exclusively spliced “flip” and “flop” exons. The two Gria genes show similar alternative exon usage within same cell types, suggesting a shared mechanism for alternative splicing. For simplicity, all genes are shown in the same orientation.