GSM8859048: MCF7_ATAC_DMSO_2d_REP1_250129_TAAGGCGA_S1; Homo sapiens; ATAC-seq
Cell pellets were resuspended in 1mL ATAC-resuspension buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2) and centrifuged at 1,000 g for 10 min at 4°C. Cell pellets were resuspended in 50μL cold lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% NP40; 0.1% Tween-20 (Roche), 0.01% Digitonin (Promega)) and incubated on ice for 3 minutes. 1mL wash buffer was added (10 mM Tris-HCl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.1% Tween-20) and cells were spun down immediately at 1,000 g for 10 min at 4°C. Following this, the pellet was resuspended in a transposase reaction mixture (2X TD buffer, 20X transposase (100nM final, Illumina), 0.01% Digitonin (Promega), 0.1% Tween-20 (Roche)) at 37 °C for 30 minutes in a thermomixer with 1,000 rpm mixing. DNA was purified using a DNA Clean and Concentrator-5 kit (Zymo) as per the manufacturer's instructions. The DNA fragments were amplified in a PCR reaction with 2X NEBNext High-Fidelity PCR Master Mix (New England Biolabs) and purified using AMPure XP beads (Beckman Coulter). DNA fragments were quantified by TapeStation 4200 (Agilent) using HSD5000 Tape and Reagent (Agilent) and Qubit (ThermoFisher). ATAC-sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) to obrain 50 million 37bp, paired-end reads.