GSM8796274: WT BMDM, 2h IFN 100U/ml, replicate2 (ATAC-seq); Mus musculus; ATAC-seq
Cells (5 × 10⁴) were lysed in 50 µL lysis buffer (10 mM Tris-HCl, pH 7.4; 10 mM MgCl₂; 0.1% Igepal CA-630) by pipetting. Nuclei were pelleted (500 × g, 10 min, 4°C), resuspended in reaction buffer (containing Tn5 transposase), and tagmented at 37°C for 60 minutes with gentle shaking. Reactions were stopped by adding cleanup buffer (900 mM NaCl, 30 mM EDTA, 2 µL 5% SDS, and 20 µg/µL Proteinase K) and incubating at 40°C for 30 minutes. Tagmented DNA was purified using 2× Agencourt AMPure XP beads. Purified DNA was PCR-amplified using HotStart KAPA HiFi enzyme. Fragments smaller than 600 bp were selected using 0.65× Agencourt AMPure XP beads, followed by 1.8× AMPure XP purification. Libraries were sequenced as paired-end 51 bp reads on an Illumina NovaSeq 6000 platform.