Illumina HiSeq 2000 sequencing
RRBS dataset to assess genome-wide DNA methylation patterns in multiple tissues from the same individual
Genomic DNA was restriction digested using Mspl, adapter ligated, size-selected (30 – 160bp), bisulfite treated with the EpiTech Bisulfite Kit (Qiagen), and PCR-amplified. Libraries were sequenced to a read length of 100bp. Raw reads were trimmed using Trim Galore v.0.3.3 and aligned to the swine reference genome (Sscrofa10.2) using BS-seeker2 v.2.0.5 with Bowtie2 v.2.1.0 in local alignment mode, with the -N option set to 1, the -L option set to 20, and allowing no more than 2 mismatches/read.