GSM8137008: ATAC-CTCF_WT_plus_rep1; Homo sapiens; ATAC-seq
ATAC-seq was performed following the protocol described previously. Nuclei were isolated from 75,000 cells in duplicate for each sample. Cell pellets were resuspended in 150 µL cold ATAC-RSB buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% TWEEN20, 0.01% digitonin and protease inhibitors) and incubated on ice for 3 minutes. One ml ATAC-RSB+ buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% TWEEN20 and protease inhibitors) was added and samples were centrifuged at 500 rpm for 10 minutes at 4°C. The nuclear pellets were resuspended in a 50 µL reaction buffer [final concentration 1X Tagment DNA Buffer (Nextera, FC-121-1030), 2.5 µL Nextera Tn5 (Nextera, FC-121-1030)] and incubated at 37°C for 30 minutes with 1,000 rpm shaking. The Qiagen MinElute PCR purification kit (Qiagen, 28004) was used to purify DNA and indexing PCR was carried out for 12 cycles with NEBNext HiFi 2X PCR Master Mix (NEB, M0541S) and indexing primers. Agencourt AMPure XP beads (Beckman Coulter, A63881) were used at a 1:3 ratio to purify DNA. The Qiagen MinElute PCR purification kit (Qiagen, 28004) was used to purify DNA and indexing PCR was carried out for 12 cycles with NEBNext HiFi 2X PCR Master Mix (NEB, M0541S) and indexing primers