GSM5066041: MTA-treated CD8 T cell -rep2; Homo sapiens; ATAC-seq
We used the OMNI ATAC-seq protocol introduced by Corces et al  for library preparation. In brief, 50,000 viable cells were pelleted (500 RCF, 4°C, 5 minutes), and lysed by resuspending in 50ul cold ATAC-Resuspension Buffer with detergents (10mM Tris-HCl; 10mM NaCl; 3mM MgCl2; 0.1% NP40; 0.1% Tween-20 and 0.01% Digitonin) and incubating for 3 minutes, followed by washing with the same buffer, but without NP40 and Digitonin. The nuclei were pelleted (500 RCF, 4°C, 10 minutes) and resuspended in 50ul transposition mix (1xTD buffer Illumina cat# 15027866), 100nM transposase (Illumina cat# 15027865), 1xPBS, 0.01% digitonin, 0.1% Tween-20). Transposition was performed at 37°C for 30 minutes in a thermomixer with shaking at 1000 r.p.m. After purification of DNA by Zymo DNA Clean and Concentrator-5 kit (cat#D4014), amplification was performed for seven cycles using NEBNext 2x MasterMix (New England Biolabs cat# M0541S). The PCR reaction was purified by double size selection with SPRI beads, to remove any primer dimers (1.3x ratio) and large fragments over 1000bp (0.5x ratio). Additional cleanups were performed to remove primer dimers, as needed.