GSM4904186: 12d-TNFa treatment+withdraw-10d+12h TNFa, ATAC-seq, rep1; Homo sapiens; ATAC-seq
45,000 cells were collected and resuspended in 50 μL cold ATAC-Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2 in sterile water) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Then the cells were incubated on ice for 3 minutes. The nuclei were washed with 1 mL cold ATAC-Resuspension Buffer containing 0.1% Tween-20 and centrifuged at 500 g and 4 ℃ for 10 minutes. The cell pellet were resuspended in 50 μL transposition mix (10 μL 5×TTBL, 5 μL TTE Mix V50, 16.5 μL PBS, 0.5 μL 1% digitonin, 0.5 μL 10% Tween-20, 17.5 μL ddH2O) with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501) and incubated at 37 ℃ for 30 minutes with shaking in a thermomixer. The reactions were cleaned up with DNA Clean & Concentrator-5 (Zymo Research D4014). The ATAC-seq libraries are prepared as previously described (Corces et al., 2017) with minor modifications. After transposition reaction, the libraries were constructed through PCR amplification with TruePrep Index Kit V2 for Illumina (Vazyme TD202) to barcode samples.