Quality assessment was based on the raw reads using the FASTQC (v0.10.1). The sequence reads (single-end 50 bp) were aligned to the rat reference genome (Rnor_6.0) with Bowtie2 (v2.0.2) using RSEM (v1.2.29) with default parameters. First, the rat reference genome was indexed using the Ensembl annotations (v83.6) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to align the reads and quantify the gene and isoform abundance. The output of rsem-calculate-expression separately gives the read count and transcripts per million value for each gene and isoform. The enrichment was at the end calculated for each biological experiment separately as summarized in data S1F. Briefly, the enrichment was defined for the odd and the even set separately, and an average enrichment was calculated across all enriched conditions.

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