ATAC-seq protocol for chromatin accessibility

ATAC-seq was performed as previously described^{57 (link)}. Briefly, cells were lysed in NLB buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.05% NP-40 and protease inhibitors (Sigma, P2714). Transposition reaction was performed on 10⁵ nuclei using 5 μl of Nextera TDEI enzyme (Illumina, FC-121-1030) for 30 min at 37 °C. DNA was then purified by Expin PCR SV (GeneAll, 103-102) and the library was amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs, M0541). The libraries were size-selected by a gel-free double-sided size-selection using Agencourt AMPure XP beads (Beckman, 63881), at 0.5X and 1.2X. Library concentration was measured by DNA High Sensitivity Kit (Invitrogen) on a Qubit fluorometer (Invitrogen). Library quality and fragment sizes were assessed on a Bioanalyzer (Agilent). ATAC-Seq libraries from two biological replicas for each condition were sequenced on Illumina Hi-seq 2000 platform.