GSM9245806: XP1139c9_60 [ATAC-seq]; Homo sapiens; ATAC-seq
For ATAC-seq, the tumors were finely chopped, washed, and were lysed using ice-cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin). Nuclei were washed again in cold lysis buffer without NP40 and Digitonin and then incubated with Tn5 transposase mixture (2.5µl of Tn5, 1% Digitonin, 10% Tween-20 in 1x TD buffer) at 370C for 30 min in a Thermomixer (Eppendorf). DNA was purified using the DNA Clean and Concentrator-5 kit (Zymo Research) and used in a PCR with Nextera adapters. ATAC-seq libraries were constructed using purified DNA and Nextera DNA Indexes by PCR.