Striatum RNA-seq from F2 Mice

Striatum punches were collected as described^{30 (link)} for RNA-seq from 23 F2 mice (all OXY-treated for historical reasons). Brains were rapidly removed and sectioned with a brain matrix to obtain a 3-mm-thick section where a 2 mm diameter punch of the striatum was collected. Left and right striatum punches were pooled and immediately placed in RNAlater (Life Technologies, Grand Island, NY, USA) for 48 h prior to storage in a −80°C freezer. Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA, USA) as described.^{30 (link)} RNA was shipped to the University of Chicago Genomics Core Facility for cDNA library preparation using the Illumina TruSeq (oligo-dT; 100 bp paired-end reads). Libraries were prepared according to Illumina’s detailed instructions accompanying the TruSeq® Stranded mRNA LT Kit (Part# RS-122–2101). The purified cDNA was captured on an Illumina flow cell for cluster generation and sample libraries were sequenced at 23 samples per lane over five lanes (technical replicates) according to the manufacturer’s protocols on the Illumina HiSeq4000 machine, yielding an average of 69.4 million reads per sample. FASTQ files were quality checked via FASTQC and possessed Phred quality scores > 30 (i.e., less than 0.1% sequencing error).