Cells were fixed with 1% formaldehyde for 15 minutes at room temperature with occasional shaking, quenched with 0.125 M glycine for 5 minutes at room temperature with occasional shaking, collected by centrifugation, (4000 g, 5 minutes), washed with cold ddH2O supplemented with EDTA-free protease inhibitors cocktail (Roche) and the pellet was resuspended in buffer Z (1 M sorbitol, 50 mM Tris 7.4, 10 mM β-mercaptoethanol) with zymolyase (Seikagaku) at 0.3 - 1 units per 1 ml of original cell volume. Cells were gently rotated at 30ºC for 25 minutes until > 95% of cells were spheroplasted. Spheroplasts were pelleted (6500 g, 10 minutes) and resuspended in NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail) at final concentration of 200 OD/ml. Chromatin was digested with 12.5 units/ml MNase (Worthington) for 20 minutes at 37ºC, and digestion was stopped by removing the tubes into ice and addition of 1 volume of ice cold MNase stop buffer ( 220 mM NaCl, 0.2% SDS, 0.2% DOX, 10 mM EDTA, 2%,Triton X-100, EDTA-free protease inhibitor cocktail). Tubes were kept on ice for 10 minutes, vortexed 3 x 10 seconds, centrifuged (16,000 g, 10 minutes, 4ºC), and the supernatant containing the nucleosomes was removed to a fresh tube. See attached paper - http://biorxiv.org/content/early/2016/06/27/060962