GSM6751420
50.000 cells per replicate were collected by centrifugation at 500 x g for 5 min at 4°C. Cell pellets were resuspended in 50 μL ice-cold lysis buffer A (see Supplementary file 1 of the manuscript) and incubated on ice for 3 min, after which 500 μL ice-cold lysis buffer B (see Supplementary file 1 of the manuscript) were added. Cell nuclei were pelleted by centrifugation at 500 x g for 10 min at 4°C. The supernatant was removed carefully and nuclei pellets were resuspended in 47.5 μL ice-cold transposition buffer and 2.5 μL Tagment DNA TDE1 enzyme (Illumina). The transposition mix was incubated at 37°C for 30 mins at 1000 rpm. After adding 20 µL 5 M guanidinium thiocyanate, tagmented DNA was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter). ATAC-Seq libraries for SK-UT-1, SK-UT-1B, MES-SA, and SK-LMS-1 were prepared in triplicate according to the Omni-ATAC protocol.