title: Hd-rR liver bisulphite whole genome sequencing
design: Genomic DNA from medaka tissue cells was isolated and sonicated to a desired size range (100–400 bp). The DNA fragments were treated with DNA polymerase to generate blunt ends and were ligated with double-stranded DNA adaptors containing methylated cytosines, which were designed to amplify only those DNA fragments carrying bisulfite-converted adaptor sequences at both ends. Followed by 7–10 cycles of PCR, 250 –450-bp size-fractionated DNA was sequenced using an Illumina GAIIx genome analyzer. Detailed experimental procedures can be found in the supplemental method section of our paper "Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns." Genome Research 22:1419-1425 (Qu et al. 2012)