GSM6475157: ATAC_CT26_Phf8 KO_1; Mus musculus; ATAC-seq
Control or Phf8 KO CT26 cells treated with or without 20 ng/mL IFN-γ for 24 hours were dissociated and 50,000 cells were washed twice in cold PBS at 4°C. ATAC-seq libraries were prepared using the N248, Illumina Nextera Kit (Novoprotein, shanghai, China).  Cells were resuspended in 50 μL cell lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.05% NP40) and incubated on ice for 5 min. Samples were then washed with 950 μL cold wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.05% NP40, 0.1% Tween 20). Samples were centrifuged at 500 g for 5 min at 4°C and supernatant were removed. The transposase reaction was carried out by titurating in 50 μL per sample in TD Buffer (10 mM Tris-HCl, pH 8, 5 mM Magnesium Chloride) with 4 μL Transposase (N248, Illumina Nextera Kit, Novoprotein, shanghai, China), and incubated at 37°C for 30 min, and 10 μL of 100 mM EDTA was added. Then, samples were incubated at 55°C for 5 min and transferred to ice. Samples and DNA recovered using Tagment DNA extract beads (N245, Illumina Nextera Kit, Novoprotein). Libraries were generated by PCR in 50 μL reaction (35 μL sample, 10 μL 5 x AmpliMix, 2.5 μL of each custom Illumina primers at 10 μM). The PCR reaction followed 72 °C for 3 min, 98°C for 30 s, followed by 9 cycles of 98°C for 15 s, 60°C for 15 s, 72°C for 8 s, followed by 72°C for 2 min. DNA was recovered using DNA clean beads (N240, Illumina Nextera Kit, Novoprotein).