GSM7400779: ATAC.24h.rep2; Mus musculus; ATAC-seq
The ATAC-seq was performed following the protocol described previously (Grandi et al. Nature Protocols 2022. 17, 1518-1552) with slight modification. Briefly, 100,000 cells were collected and washed once with DPBS, and nuclei were isolated by incubating the cells with 50 μl ice-cold ATAC-RSB buffer (10 mM Tris-HCl pH 7.6, 10mM NaCl, 3mM MgCl2) with 0.1% NP40, 0.1% Tween 20, and 0.01% Digitonin for 3 minutes on ice. The nuclei were then washed once with ATAC-RSB buffer with 0.1% Tween 20 and incubated with 50 μl transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (120 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O) at 37°C for 30 minutes and mixed in thermomixer at 1000 RPM. The transposition was stopped by adding 250 μl (five volumes) DNA binding buffer to the transposition mix and DNA was purified with Zymo DNA Clean and Concentrator-5 Kit (D4014) and eluted in 21 μl elution buffer. For library preparation, 5 cycle of pre-amplification was performed, and the DNA concentration was then quantified, followed by an additional 5 cycles of amplifications. The library DNA was purified with Zymo DNA Clean and Concentrator-5 Kit and eluted in 20 μl of H2O.