MNase-seq of MRE11 4 h (replicate 1)
MNase-seq as previously described (Kubik et al., 2018, pmid: 29979971) with modifications. Briefly, after spheroplasting and MNase digest, we treated with RNase and Quick-CIP (NEB). We isolated the mononucleosomal band by gel extraction, phenol-chloroform extraction, and ethanol precipitation. We then prepared paired-end TruSeq libraries by end repair, A-tailing, and ligation of forked TruSeq adapter fragments using NEB's NEBNext End-repair module, Klenow 3'-5' exo^-, and T4 DNA Ligase, respectively, using SPRI beads for clean-up between each step. We used KAPA HiFi DNA Polymerase (Roche) for low cycle library amplification. We performed final size selection by gel extraction, phenol-chloroform extraction, and ethanol precipitation.