GSM5904684: HCT116 FOXD2 ATAC rep2; Homo sapiens; ATAC-seq
ATAC lysis buffer (10mM Tris-HCT pH7.4, 10mM NaCl, and 3mM MgCl2 containing 0.1% NP40, 0.1% Tween-20, and 0.01% Triton-X 100) We lysed 50,000 cells of interest with 50 μl lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% Triton X-100) and incubated them for 10 min on ice. Following centrifugation at 1,000g for 10 min at 4 °C, we resuspended nuclei pellets with 50 μl of transposition mix (25 μl 2× TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20% dimethyl formamide in sterile water) and 2.5 μl transposase (100 nM final concentration), 16.5 μl PBS, 0.01% Triton X-100, 0.1% Tween-20 and 5 μl H2O) and incubated the mixture with shaking for 1 h at 55 °C in a thermomixer. We purified transposed DNA using DNA Clean and a Concentrator-5 Kit (Zymo Research) then amplified it using the NEBNext High-Fidelity 2× PCR Master Mix for 10 cycles. Subsequently, we then performed ATAC-seq using the Illumina NovaSeq600 dual indexed platform.