GSM7695953: MV411_ATACseq_8h_DMSO_rep1; Homo sapiens; ATAC-seq
ATAC-seq was performed as described in Grandi et al., (PMID: 35478247) with some modifications. Briefly 100,000 cells were mixed with 10,000 S2 Drosophila cells, and pelleted at 500g for 5 minutes at 4°C. Cells were washed with 100 µL ice cold DPBS (Corning 21-031-CV), and pelleted at 500g for 5 minutes at 4°C. The cell pellet was resuspended in 50 µL of ATAC-seq Lysis Buffer (0.1% NP40, 0.1% Tween-20, 0.01% digitonin, 10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2) and incubated on ice for 3 minutes. Then 1 mL of ATAC-seq Wash Buffer (0.1% Tween-20, 10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2) was added to dilute the lysis reagents, and nuclei were pelleted by spinning at 500g for 19 minutes at 4°C. Nuclei were then resuspended in 50 µL Transposition Mix (1X Tagment DNA Buffer, 0.33X DPBS, 0.01% digitonin, 0.1% Tween-20) treated with 3 µL TDE1 Tagment DNA Enzyme (Illumina 20034197). The reaction was incubated at 37°C for 30 minutes shaking at 1,000 rpm. Tagmented DNA was subsequently purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, cat. no. D4014). Purified samples were combined with NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs M01541) for amplification. As described in Grandi et al., (PMID: 35478247), custom primers were used to incorporate Illumina adaptors and index sequences into sample fragments.