To characterize the effects of chronic cocaine and withdrawal on mRNA expression in the NAc, we prepared mRNA-Seq libraries from RNA pooled from mice subjected to daily saline injections (Saline), daily cocaine injections (Cocaine) or daily cocaine injections followed by a week with no injections (Withdrawal). Paired-end sequencing yielded approximately 20 million uniquely mapped reads for each library (Table 1A). The current annotation of the Mus musculus genome (2007, mm9) spans ~1.6 billion bases; 3.2% of the genome encodes mature mRNAs and 40.6% encodes primary transcripts. We detected 5–6% of the genome in the poly(A)+ RNA-Seq data from each NAc library. Approximately 80% of the reads in each library mapped to annotated exons; 15–16% of reads mapped to introns and 5% of reads aligned to intergenic regions (Table 1B). Mitochondrial reads accounted for roughly 2% of all mapped sequences in these libraries (Figure S2). Scatter plots of mitochondrial (Figure S3) and ribosomal (Figure S4) gene expression demonstrated no evidence for cocaine-regulation, so subsequent analyses were performed on a filtered gene list that excluded both ribosomal and mitochondrial genes.
