Illumina HiSeq 2500 sequencing; Whole genome bisulfite sequencing of bovine oocytes from metabolically divergent lactating cows and nulliparous heifers
Oocytes were collected from cows using transvaginal ultrasound-guided ovum pick-up (OPU). Using an ultrasound probe system (General Electric) with a cannula connected to an aspiration pump (Minitube), subordinate follicles of size smaller than 8mm were aspirated. Oocytes were mechanically denuded using hyaluronidase and snap frozen. Pooled oocytes were lysed and bisulfite treated using the EZ-DNA Methylation-Direct Kit (Zymo Research) following manufacturer's instructions.  Sequencing libraries were generated from the bisulfite treated DNA using the Pico Methyl-Seq Library Prep Kit (Zymo) according to manufacturer's recommendations with 20µM PrepAmp primer mix and 10-cycle PCR amplification.