RNA-seq and Heatmap generation

RNA sequencing libraries were generated by using a TruSeq stranded mRNA library prep kit and sequenced using Illumina HisEq 2000. Single-end RNA-seq reads were mapped to the reference mouse genome (mm10) using TopHat v.2.1.0 (Trapnell et al., 2012). Transcript quantification and differential expression analysis were performed by Cufflinks v2.2.1 and Cuffdiff 2, respectively (Trapnell et al., 2012). For differentially expression analysis, the fold-change cutoff was set at 1.5 or higher. Benjamini-Hochberg false discovery rate adjusted P value less than 0.05 was considered statistically significant. Heatmaps were generated by GENE-E (https://software.broadinstitute.org/GENE-E/index.html) using RPKM output from Cufflinks. Rows were clustered using Pearson correlation metric and average linkage.