RNA Extraction and Sequencing Protocol

RNA extraction and sequencing was performed as previously described^{85 (link)–87 (link)}. Briefly, total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. The quality of the RNA was assessed using the Tapestation 2200 (Agilent) and Libraries prepared using TruSeq Library prep kits (Illumina), and then run on the Tapestation high sensitivity DNA assay kits to ensure correct library size. Libraries were quantified using the Qubit® 2.0 Fluorometer, pooled and run on the Hiseq 2500 (Illumina). Reads were mapped to the mouse transcriptome using Bowtie2 algorithm^{88 (link)} and counted as reads per gene using RSEM^{89 (link)} and then analyzed using the statistical algorithm limma. Genes were then sorted by their posterior error probability (local false discovery rate, FDR). We also express significance of a gene as the q value, which is the smallest false discovery rate at which a gene is deemed differentially expressed. All RNA-seq data can be found at Gene Expression Omnibus (GEO) database, [http://www.ncbi.nlm.nih.gov/geo] (accession GSE119772).