ChIP libraries were prepared using the NEBNext DNA Sample Prep Master Mix Set 1 according to the manufacturer’s specifications, but with the following amendments: end repair was carried out using 5 μl of NEBNext End Repair Reaction Buffer and 0.5 μl of NEBNext End Repair Enzyme Mix. A-tail was carried out using 5 μl of NEBNext A-tail Reaction Buffer and 0.3 μl of NEBNext Klenow Fragment (3′→5′ exo-) Enzyme Mix. Ligation was carried out using 10 μl of NEBNext Quick Ligation Reaction Buffer and 0.5 μl of NEBNext Quick T4 DNA Ligase Enzyme Mix. The NEBNext adapters were diluted 100-fold, and the amount added was adjusted if less than 5 ng of ChIP material was available. No size selection was carried out. PCR was done using the following reaction mix with 18 cycles of PCR: DNA (36 μl), 5× Phusion buffer (10 μl), custom paired end (PE) primer 1 (1 μl), custom PE primer 2 (1 μl), dNTP (deoxynucleotide triphosphate) mix (1.5 μl), Phusion polymerase (0.5 μl). The cleanup after amplification was done at 1:0.85 (AMPure beads/DNA). The concentration of
