Material	Manufacturer
RNase A, DNase and protease-free	Thermo Scientific
DNA Polymerase I, Large (Klenow) Fragment	New England Biolabs
T4 DNA Polymerase	New England Biolabs
T4 Polynucleotide Kinase	New England Biolabs
Klenow Fragment (3´→5´ exo–)	New England Biolabs
Phusion High-Fidelity DNA Polymerase	New England Biolabs
HpaII	New England Biolabs
HinP1I	New England Biolabs
AciI	New England Biolabs
HpyCH4IV	Thermo Scientific
Bsh1236I	New England Biolabs
Deoxynucleotide Solution Mix	New England Biolabs
Denosine 5´-Triphosphate (ATP)	New England Biolabs
dATP solution	New England Biolabs
T4 ligase reaction buffer (10×)	New England Biolabs
Quick Ligation Kit
Agencourt AMPure XP beads	Beckman Coulter
Monoclonal Antibody against 5-Methylcytidine	Eurogentec
AffiniPure Rabbit Anti-Mouse IgG, Fcγ	Jackson ImmunoResearch
Fragment Specific
Protein A/G agarose beads	Fisher Scientific
Phase lock gel light (2 ml)	5 PRIM
Phenol/chloroform/isoamyl alcohol	Roche
Chloroform	Sigma-Aldrich
Sodium Acetate, pH 5.5 (3 M)	Life Technologies
Ethanol	Sigma-Aldrich
Qubit dsDNA HS Assay Kit	Life Technologies
Agarose, Molecular Biology Grade	VWR
Ethidium bromide	BioExpress
TAE 50× Reagent	5 PRIME
Orange DNA loading dye (6×)	Thermo Scientific
2-Log DNA ladder	New England Biolabs
MinElute PCR Purification Kit	Qiagen
Isopropanol	Sigma-Aldrich
iTaq universal SYBR Green supermix (2×)	Bio-Rad