Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies. ChIP DNA samples was used in a 23.3 μl combined end repair and A-tailing reaction using a KAPA Hyper Prep Kit (Kapa Biosciences) for 30 minutes at 20°C followed by 30 minutes at 65°C. 10 μl of ligase buffer, 3.7 μl of Adapters and 3.3 μl ligase (KAPA Hyper Prep Kit) were added and incubated at 20°C for 4 hours. Double-stranded DNA fragments were purified from this reaction using KAPA Pure Beads (Kapa Biosciences) and eluted in 22 μl 10 mM Tris pH8.0. Libraries were generated by PCR and size-selected on a 2% E-Gel EX agarose gel (Invitrogen) and fragments between 150 and 400 bp were extracted using a QIAEX II Gel Extraction Kit (Qiagen) performed at room temperature.