Agilent tapestation genomic dna kit

Enhanced reduced representation bisulfite (ERRBS) was performed at the University of Michigan Epigenomics Core as described previously (Akalin et al. 2012 (link); Garrett-Bakelman et al. 2015 (link)). Briefly, $75\text{ng}$ of genomic DNA was digested using MspI, a restriction enzyme that preferentially cuts CG-rich sites. The digested DNA was then purified using phenol:chloroform extraction and ethanol precipitation in the presence of glycogen, before blunt-ending and phosphorylation. A single adenine nucleotide was next added to the 3′ end of the fragments in preparation for the ligation of the adapter duplex with a thymine overhang. The ligated fragments were cleaned, then processed for size selection on agarose gel. Selected fragments were treated with sodium bisulfite to convert unmethylated cytosines to uracils, which are then replaced with thymines during PCR amplification. After cleanup with AMPure XP beads (Product #A63880; Beckman Coulter), libraries were quantified using the Agilent TapeStation genomic DNA kit (Catalog #G2991AA; Agilent) and Qubit broad range dsDNA (Catalog #Q32850; Invitrogen). Single-end, $50\text{-bp}$ reads were obtained for each library by sequencing on the HiSeq 4000 system (Illumina). ERRBS samples were multiplexed, with three samples per sequencing lane.