RNA-Seq of Rattus norvegicus: whole brain treted with rexinoids
Male SpragueDawley rats (812 weeks old and 250350 g, obtained from Harlan Laboratories, Indianapolis, IN) were allowed to acclimate for over 2 days, fasted 24 h prior to a single dose of rexinoid solubilized in sesame oil at a target concentration 100 mg/kg and then allowed to feed ad libitum 4 h post dose (Harlan Certified Rodent Diet #2016C or 2016CM and clean water). Dosing was done by oral administration using a blunt needle. Brains from animals treated above were removed and snap frozen in liquid nitrogen and then sent to LabCorp Clinical Trials (formerly Covance Genomics Lab) where they were suspended in 500 L of RLT buffer (Qiagen, Valencia, CA) containing -mercaptoethanol and homogenized using a Covaris homogenizer (Woburn, MA). Following trizol/chloroform treatment, RNA was extracted using Promega SV96 isolation kits. RNA_Seq libraries were constructed using Illumina's TruSeq Total RNA strand specific kits (San Diego, CA) with 250 ng of total RNA. Initial FASTQ files were subjected to quality control with the FastQC tool.