RRBS data from Bubalus bubalis rumen
After quantification of DNA samples with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA), 100 ng of high-quality DNA from each sample was used as input for library generation using the Ovation RRBS Methyl-Seq System (NuGEN, Redwood City, CA), following the manufacturers instructions. Briefly, DNA was digested with the methylation insensitive restriction enzyme MspI, which recognizes CCGG, ligated to sequencing adaptors, repaired, converted with bisulfite, and amplified by PCR (7 cycles of PCR). Unmethylated lambda phage DNA was spiked-in to estimate the bisulfite conversion rate. The concentration of the final libraries was measured with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Caliper GX DNA Assay (PerkinElmer, Waltham, MA). Libraries were then sequenced in single-end mode of 100 bp, 20 M reads per sample, using a NovaSeq6000 (Illumina, San Diego, CA). The processing of raw data for both format conversion and de-multiplexing was performed by Bcl2Fastq 2.20 version of the Illumina pipeline.