title: GSM5736478: muscle02; Bos indicus; Bisulfite-Seq
library_construction_protocol: DNA extraction was carried out using the DNeasy® Blood & Tissue kit (Qiagen Inc., Germantown, MD, USA), according to the manufacturer's protocol. DNA concentration was measured using Qubit dsDNA High Sensitivity Assay (Thermo Fisher Scientific Waltham, MS, EUA) and the quality measured by Fragment Analyzer™ and the DNF-487 Standard Sensitivity or the DNF-488 High Sensitivity genomic DNA Analysis Kit (Advanced Analytical). Each sample library was prepared from 100 ng of genomic DNA using the Premium RRBS kit (Diagenode), according to the manufacturer's protocol. Bisulfite conversion efficiency independent of CpG context was assessed by adding methylated and unmethylated spike-in controls (0.1% concentration). Briefly, the protocol consists in the digestion of DNA by MspI enzyme followed by the fragment end repair, and addition of adaptors. Next, samples were quantified by qPCR and the Ct values were used to pool samples by similarity. Bisulfite conversions were performed using the Premium RRBS kit (Diagenode) followed by library enrichment by PCR, based on the manufacturer's protocol. Adequate fragment size distributions were confirmed by Bioanalyzer High Sensitivity DNA chips (Agilent). Libraries were sequenced on Illumina HiSeq 3000 using single-end 50 bp reads.