GSM8078013: BxPC3,plusIFNγ, Replicate8, ATAC-seq; Homo sapiens; ATAC-seq
ATAC-seq was performed using homemade transposomes with minor modifications that are detailed below (Buenrostro et al.,2013; Picelli et al., 2014)). For each replicate, we trypsinized, washed, and resuspended 250,000 cells in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40, 0.1% tween-20, 0.01% digitonin) and lysed for 10 minutes on ice (Corces et al., 2017). After lysis, 50,000 cells were resuspended in transposase reaction mix (1ul Tn5 (0.5 µM), 4ul 5X TD-TAPS (50mM TAPS-NaOH, 25mM MgCl2, 50% DMF), 5ul dilution buffer (10mM Tris-HCl, pH 7.4, 100mM NaCl, 1mM DTT, 50% glycerol), 2ul 10% Tween, and 8ul PBS) and tagmentation was performed at 37°C for 30 minutes. Next, samples were purified using the Zymo Clean and Concentrate kit. For the library preparation, DNA was amplified with NEBNext High-Fidelity 2× PCR Master Mix as previously described (Buenrostro et al.,2013). The PCR program was as followed: 72 °C for 5 minutes, 98 °C for 30 seconds, (98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 60 seconds) x 12 cycles. Samples were sequenced on both Illumina NextSeq 500 and Ultima Genomics platforms.