RNA sequencing and analysis were carried out as previously reported (McClintick et al., 2015). We first used SOLiD™ Instrument Control Software and SOLiD™ Experiment Tracking System Software for the read quality recalibration. Sequences containing more than two ‘N’ were discarded. If a 5 base sliding window had an average quality score less than 20, the read was truncated at the beginning of that 5-base window. Reads with fewer than 35 bases were discarded. Reads that passed these filters were mapped to the rat genome (rn4) using the BFAST algorithm (Homer et al., 2009). We used a Tophat-like strategy (Trapnell et al., 2009) to align the sequencing reads on both exonic regions and across junctions. The expression levels of each isoform were counted using NGSUtils (Breese and Liu, 2013), normalized to the total number of sequencing reads falling into annotated gene regions in each sample, and further scaled based on a trimmed mean of log transformed counts per million (CPM) value to correct for the variability of RNA composition in each sample (Robinson and Oshlack, 2010). The scaled CPM was used
