GSM5665759: DND41ResCas9_bioRep2_ctrl_ATAC_rep4; Homo sapiens; ATAC-seq
ATAC-seq was performed as previously described (Buenrostro et al., 2013) and three replicates were performed for each condition. Briefly, 50,000 cells were pelleted at 800 x g and washed with 50 μl of ice cold 1 x PBS (Corning cat# 21031CV), followed by 2min treatment with 50 μl lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% Igepal cat# CA-630). Pelleted nuclei were resuspended in 50 μl of transposition buffer (25 μl of 2 x TD buffer, 22.5ul of molecular biology grade water and 2.5 μl Tn5 transposase (Illumina cat# FC-121-1030) to tag the accessible chromatin for 45min at 37°C. Tagmented DNA was purified with MinElute Reaction Cleanup kit (Qiagen cat# 28204) and amplified with 5 PCR cycles. Additional number of PCR cycles was determined from the side reaction and ranged from 10-12 total cycles of PCR. Libraries were purified using QiaQuick PCR purification kit (Qiagen cat# 28106) and eluted in 20 μl EB buffer. Indexed libraries were assessed for nucleosome patterning on TapeStation 4150 (Agilent) and paired-end sequenced (38bp+38bp) on Illumina NextSeq 550.