All 101-bp paired-end sequence reads were preprocessed by eliminating adaptor sequences and low quality reads using BBDuk in BBMap version 34.90 (https://jgi.doe.gov/data-and-tools/bbtools/). Cleaned sequence reads were mapped to the rat transcriptome (Ensembl Rnor_6.0) using Bowtie2 version 2.2.5 (Langmead and Salzberg, 2012) and RSEM package version 1.2.21 (Li and Dewey, 2011). Finally, differentially expressed genes (DEGs) were identified using EBseq in the R package (Leng et al., 2013). Significantly different mRNA expression was defined as a fold change threshold of 2 and a posterior probability of a differential expression (PPDE) threshold of 0.95.

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