Enrichment was performed using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) according to the manufacturer’s protocol with the following changes:
Used 25uL of Dynabeads M-280 (10uL/ug of input DNA) and 15uL of MBD-Biotin Protein (7uL/ug of input DNA).
Followed the corresponding instructions for the volumes listed above and for quantities of input DNA > 1ug - 10ug
A single elution with 2000mM NaCl was performed
EtOH precipitation: Samples were incubated over the long weekend at -80C.