GSM8118538
30 min before harvest, cells were treated with 200 units/ml DNase (Sigma, DN25). HEK293 cells were then washed twice with PBS (Gibco, 10010023) and detached with TrypLE (Gibco, 12605010). Enzymatic digestion was quenched with growth medium and cells were washed once again with PBS. ATAC libraries were prepared from 50 000 cells per sample according to the published OmniATAC protocol (Corces et al., 2017) with minor adaptations. In short, samples were washed with cold 50 ul of PBS, afterwards cells were incubated in 50 ul lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) for 3 min on ice. Cells were washed with 1 ml of lysis buffer without Digitonin and NP-40. Transposition was done in 50 ul reaction buffer (1x tagmentation buffer (Diagenode, C01019043), 0.1% Tween-20, 0.01% and 2.5 ul Tn5 (Diagenode, C01070012)) for 30 min at 37 Celsius and 1000 RPM shaking. Subsequent DNA purification was performed with MinElute Reaction Cleanup Kit (Qiagen, 28204). PCR amplification was done with NEBNext High Fidelity 2X PCR Master mix (NEB, M0541) and UDI primer (Diagenode, #C01011034) with concentrations according to manufacturer's recommendation. Total number of needed amplification cycles (8x) was controlled with qPCR. Library purification and fragment size selection was done with AMPure XP beads (Beckmann, A63880). 20 ul of 10 nM was sent for sequencing externally with Novogene (Cambridge, UK). A minimum of 20 Mio PE reads were sequenced per sample.