Genomic DNA was extracted as described in Chun and Madhani, Methods Enzym. 2010. ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNA was isolated by antibodies directed to our proteins of interest (10 mg of anti-Histone H3, 10 mg anti-FLAG M2, or 4 mg of anti-Cse4).  DNA was then isolated by incubation with SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns). ChIP-seq: Described in Homer et al. 2016 Bisulfite-seq: Described in Urich et al., 2015 MeDIP-seq: the initial step as described in Urich et al., 2015 with the exception that unmethylated adapters were ligated to repaired, dA-tailed DNA.
GEO Accession
GSM3963379