ATAC-seq was performed on 50,000 cells as described previously with minor modifications (Buenrostro et al. 2013). Cell suspensions were thawed at 37°C and pelleted for 5 min at 500 g at 4°C. Cell pellets were resuspended in 250 µl permeabilization buffer (5 % BSA, 0.2 % IGEPAL-CA630, 1mM DTT and cOMplete EDTA-free protease inhibitor cocktail (Roche) in PBS) and incubated on an overhead shaker for 5 min at 4°C, followed by centrifugation for 5 min at 500 g. Pellet was resupended in 25 µl tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM K-acetate, 11 mM Mg-acetate, 17.6 % DMF) and counted on a hemocytometer.  40K nuclei were used for tagmentation and the reaction volume was adjusted to 19 µl using tagmentation buffer. After addition of 1 µl Tn5 transposomes (Illumina) tagmentation was performed at 37°C for 60 min with shaking (500 rpm). Next, samples were purified using MinElute columns (Qiagen), PCR-amplified for 9 cycles with NEBNext® High-Fidelity 2X PCR Master Mix (NEB, 72°C 5 min, 98°C 30 s,[ 98°C 10 s, 63°C 30 s, 72°C 60 s] x cycles, 72°C ∞). Amplified libraries were purified using MinElute columns (Qiagen) and Ampure XP Bead (Beckmann Coulter).
GEO Accession
GSM3262985