Figure 5.

Alternative splicing analysis of neurons, glia and vascular cells. A, Six types of alternative splicing events are detected by RNA-Seq. Boxes and black lines represent exons and introns, respectively. Blue lines and red lines represent alternative splicing events detected in the dataset. The 5′ end is to the left, and the 3′ end is to the right. Cassette, The inclusion or exclusion of an exon; Tandom Cassette, the inclusion or exclusion of two or more tandom exons; Mutually Exclusive, the inclusion of one exon in one transcript and inclusion of a different exon in another transcript; Intron Retention, the inclusion or exclusion of a segment previously annotated to be an intron; Alternative 5′ SS, the alternative usage of a splicing site on the 5′ end of an exon; Alternative 3′ SS, the alternative usage of a splicing site on the 3′ end of an exon. B, Frequencies of the six types of alternative splicing events detected in the entire dataset and in individual cell types. In all cell types, cassette exon events, i.e., the inclusion or exclusion of an exon, are the most frequently detected alternative splicing events. C, The numbers of genes that are alternatively spliced in each cell type and the union of these samples. The dotted line represents the total number of genes that are known to contain a potential splicing event in the mouse genome. The number of these genes that are expressed in a given cell type are represented by gray bars. The black bars indicate the numbers of genes that are alternatively spliced in a given cell type based on criteria outlined in Materials and Methods. D, The numbers of statistically significant cell type-specific alternative splicing events in each cell type. Neurons have the highest number of specific splicing events, whereas oligodendrocyte-lineage cells have the least amount of specific splicing events. E, Pkm2 is an example of a gene spliced uniquely in astrocytes and neurons. The traces represent raw data of the number of reads mapped to the Pkm2 gene from astrocytes and neurons. The height of the blue bars represents number of reads. The bottom schematic is the transcript model of Pkm2 gene from the UCSC Genome Browser. Boxes represent exons, and black lines represent introns. The exon shown in blue is predominantly included in neurons, whereas the exon shown in yellow is included only in astrocytes. This is an example of a mutually exclusive event. F, Validation of PKM1/2 splicing differences by PCR. We designed primers targeting exons unique to PKM1, unique to PKM2, and exons common to PKM1 and PKM2. PCR products were detected from neuron, astrocyte, and whole-brain samples in patterns predicted by the RNA-Seq data.