GSM7033895: Hudep-2 MBD2 KO, replicate 2; Homo sapiens; ATAC-seq
50,000 cells of expansion phase HUDEP-2 or derived cell lines were collected, and permeabilized with 50 μL ice cold lysis buffer (10 mM Tris-HCL pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) for 3 min. The transposition reaction was carried out at 37°C for 30 minutes in 50 μL volume containing 25 μL 2× TD buffer and 2.5 μL Tn5 Transpose enzyme (Illumina). DNA was purified with Qiagen MinElute PCR purification kit (Qiagen). Library amplification was performed with NEBNext Ultra II Q5® Master Mix (contained in NEBNext® Ultra™ II DNA Library Prep Kit). PCR amplification was carried out as follow: 72°C 5 min, 98°C 30 s, 98°C 10 s, 63°C 30 s, 72°C 1 min, repeat steps 3-5 for another 4-6 cycles, hold at 4°C. The resulting libraries were purified using AMPure XP beads (Beckman Coulter) and quantified with Qubit fluorometer and bioanalyzer, and then sequenced in NextSeq 500 platform 76 bp single read sequencing.