Library formation (polyA+, stranded) and sequencing were all performed according to Illumina’s (San Diego, CA) specifications at the OHSU Massively Parallel Sequencing Shared Resource. Libraries were multiplexed 6 per lane, yielding approximately 25–30 million total reads per sample. FastQC was used for quality checks on the raw sequence data. Sequence data were then aligned using STAR [Spliced Transcripts Alignment to a Reference, 2.3.0e (Dobin et al. 2013)] allowing for a maximum of three mismatches per 100 bp read. For all samples, >85% of the reads were uniquely aligned. Using the Bedtools suite (2.26.0), reads were aligned to known genomic features to generate counts at the gene and exon level. Gene and exon expression data were imported into the R application environment; upper-quartile normalization was performed using the edgeR Bioconductor package (Robinson et al. 2010). The read density threshold for inclusion in the network analyses for genes and exons was 30 and 5, respectively. Network connectivity for both coexpression and cosplicing were calculated as described elsewhere (Iancu et al. 2015). Genes in the top 50% for both coexpression and cosplicing connectivity
