title: BS-Seq of Chinese alligator, female ovary, warmroom, winter
design: The gDNA was spiked with non-methylated  DNA fragments for bisulfite conversion quality control purposes. For each sample, 6 mg gDNA and 30 ng  DNA were mixed and fragmented into 200300 bp using sonication. After end repair and acetylation, barcodes with methylated cytosines were added to the fragmented DNA. DNA bisulfite conversion was carried out twice using an EZ DNA methylation-GoldTM Kit (Zymo Research, Irvine, CA). The DNA fragments were then amplified by PCR using KAPA Hifi HotStart Uracil+ ReadyMix (Kapa Biosystems, Wilmington, MA). The index-coded samples were clustered using a TruSeq PE Cluster Kit v3-cBot-HS on a cBot Cluster Generation System (Illumina) according to the manufacturers instructions. The BS library was sequenced on the Illumina HiSeq 2500 platform, generating 125-bp paired-end reads.