The DNA methylome data generated using MeDIP-Seq technique from pig loin.

loin samples from four pairs of Duroc gilt littermates, with an average body weight of 101.6 ± 5.3 kg and average age of 184 ± 9 days, were collected from commercial breeding farms after slaughter.Genomic DNA was extracted from LDM samples and isolated using the phenol-chloroform-isoamyl alcohol method as follows: firstly, LDM tissue was frozen in liquid nitrogen, crushed with a mortar and pestle, and digested for 12 hr at 55 °C in a lysis buffer and 0.1 mg/ml of proteinase K. At the end of the incubation, 5 ml of protein PPT buffer was added to precipitate proteins without heating. After centrifugation of the solution at 13,000 rpm for 10 min, the supernatant was collected in a clean tube and 5 ml of phenol-chloroform-isoamyl alcohol (25:24:1) was added. After a further centrifugation at 13,000 rpm for 15 min, 5 ml of the aqueous phase was transferred to a clean tube, and the DNA was precipitated using 0.5 ml of 3 M sodium acetate and 10 ml of 100 % ethanol. The pellets were washed with 70 % ethanol, allowed to dry, and dissolved in TE buffer.For each sample, 1.2 μg of genomic DNA was randomly sheared to approximately 200–300 bp fragments using a Covaris S2. MeDIP libraries were constructed using the TruSeq DNA Sample Prep kit (Illumina, San Diego, CA, USA) following the manufacture’s recommended protocol. The DNA fragments were end-repaired, phosphorylated, poly(A)-tailed, and then ligated with Illumina single read adapters. The adapter-ligated DNA fragments sized approximately 250­–300 bp were screened by gel electrophoresis and purified with MinElute Gel Extraction kit (Qiagen, Valencia, CA, USA), and were used for MeDIP enrichment using Methylated DNA Immunoprecipitation kit (Diagenode, Liège, Belgium) following the manufacture’s recommendation. The immunoprecipitated DNA fragments were then PCR amplified: 98 °C for 30 sec; 10 cycles of 98 °C for 10 sec, 60 °C for 30 sec and 72 °C for 30 sec; and 72°C for 5 min. MeDIP libraries were quantified using Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, Carlsbad, CA, USA). Flow cells were prepared with 8 pM DNA using the manufacture’s recommended protocol and sequenced on an Illumina Genome Analyzer II to generate single-end 36 bp reads.