DNA methylation of rainbow trout muscle under variable ploidy and muscle mass conditions
Methyl-MiniSeq Library preparation: 500 ng of starting input genomic DNA was sequentially digested with 60 units of TaqI followed by 30 units of MspI (NEB) and then purified with Zymo Research DNA Clean & Concentrator-5 (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5-methyl-cytosine instead of cytosine according to Illuminas specified guidelines. Adaptor-ligated fragments of 150-250 bp and 250-350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel using Zymoclean Gel DNA Recovery Kit (Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning Kit (Cat#: D5030). Preparative-scale PCR was performed and the resulting products were purified with DNA Clean & Concentrator-5 (Cat#: D4003) for sequencing on an Illumina HiSeq.