Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation

. Author manuscript; available in PMC: 2016 Jan 15.

Published in final edited form as: Methods. 2014 Nov 6;72:29–40. doi: 10.1016/j.ymeth.2014.10.032

Oligonucleotide	Sequence
adapter: PE 1.0	ACACTCTTTCCCTACACGACGCTCTTCCGATC^*T
adapter: PE 2.0	P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
PCR primer: PE 1.0	AATGATACGGCGACCACCGAGATCTACACTCTTTC CCTACACGACGCTCTTCCGATCT
PCR primer: PE 2.0	CAAGCAGAAGACGGCATACGAGATNNNNNNNGTG ACTGGAGTTCAGACGTGTGCTCTTCCGA
SNRPN-F	CGCTCAACACCCCCTAAATA
SNRPN-R	GGTGGAGGTGGGTACATCAG
GABRB3-F	CCTGCAACTTTACTGAATTTAGC
GABRB3-R	GGAATCTCACTTTCACCACTGG
qPCR primer 1.0	AATGATACGGCGACCACCGAGAT
qPCR primer 2.0	CAAGCAGAAGACGGCATACGA

Asterisk * indicates a phosphorothiate linkage, P indicates a phosphate group, and N indicates index code. The 5-terminal phosphate in adapter PE 2.0 facilitates the ligation of annealed adapters to DNA inserts. The phosphorothiate linkage in adapter PE 1.0 prevents nuclease cleavage of the T overhang, which is required for the adapter and A-tailed DNA fragment ligation.