GSM5584800: Jurkat T cells-ATAC_TNF_rep2; Homo sapiens; ATAC-seq
50,000 suspension cells were collected per sample and input for ATAC-seq library preparation. ATAC-seq was performed using the OMNI-ATAC protocol (Corces et al.). After counting 50,000 cells/library, nuclei were isolated with Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. The purified Jurkat or J-Lat nuclei were then resuspended in a transposase reaction containing 0.05% digitonin and incubated for 30 min at 37 °C. Following incubation, samples were treated with Proteinase K at 55 °C for 2 hr, and genomic DNA was isolated via phenol:chloroform:isoamyl alcohol and EtOH precipitation. Library amplification was done with 2x KAPA HiFi mix (Kapa Biosystems) and 1.25 µM indexed Illumina primers using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and 10-11 cycles at 98 °C for 10s, 63 °C for 30 s, and 72 °C for 1 min. Libraries were generated with two biological replicates per condition sampled.