title: GSM7025404: GCB_K_rep4 [KKO_R4]; Mus musculus; ATAC-seq
library_construction_protocol: 60,000 freshly sorted live cells were washed in cold PBS, lysed in 60 ul cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) for 3 min on ice, followed by addition of 1 ml wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and centrifugation to pellet nuclei. Bulk ATAC-seq libraries were prepared following the Omni-ATAC protocol. Briefly, nuclei were resuspended in a transposition reaction mix prepared using the Illumina Tagment DNA Enzyme and Buffer Kit (Illumina, 20034197) and incubated at 37 ºC for 30 minutes on thermomixer at 1,000 rpm to allow for transposition-based DNA fragmentation and adapter ligation. Tagged DNA fragments were purified using the Clean & Concentrator-5 Kit (ZYMO, D4014), then subjected to PCR amplification and double-sided bead purification (to remove primer dimers and larger than 1,000 bp fragments) using the AMPure XP beads (Beckman Coulter, A63881).