Total RNA was isolated from frozen tissues using a Qiagen miRNeasy Kit (Valencia, CA) according to the manufacturer’s protocol. Thermo Scientific Nanodrop 2000 (Waltham, MA) and an Agilent 2100 Bioanalyzer (Santa Clara, CA) were used to evaluate RNA purity and integrity. A minimum RNA integrity value of 7.0 was required for RNA samples to be used for library preparation and sequencing. Total RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq Total RNA Sample Prep Kit (Illumina, Inc., San Diego, USA) with ribosomal depletion. Paired-end (50bp) sequencing was performed using the Illumina HiSeq 2500 instrument; Supplemental Table 1). Reads were filtered (score of 20 or greater in at least 90 percent of nucleotides), adapters removed, and aligned to appropriate reference genomes (C57BL/6: NCBI Build 37; CAST/EiJ: Build 37 pseudogenome (http://csbio.unc.edu/CCstatus/index.py?run=Pseudo) using STAR (Wu and Nacu 2010 (link)). Transcript quantification was performed using RSEM (Li and Dewey 2011 (link)). Further details on data processing pipeline are described in (Chappell et al. 2017 (link)).