Raw reads in the FASTQ format were controlled for quality using Trimmomatic (69). Trimmed reads were then aligned to the mouse genome (University of California Santa Cruz Mouse Genome Browser mm9) using TopHat v.2.1.0 (70). Only uniquely mapped reads with a maximum of two mismatches over the whole length of the gene were considered for ensuing analyses. Gene annotations came from Ensembl release 75. Exonic reads were assigned to specific genes from Ensembl release 75 using the htseq-count script from HTSeq-0.6.1 (71).

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