GSM7498548: K562, CUX1_KO, rep2; Homo sapiens; ATAC-seq
For all experiments, K562 cells were harvested from cultures at ~60% confluency and primary CD34+ HSPCs were harvested 48 hours post transfection. For both K562 and primary CD34+ HSPCs, 50,000 cells were lysed using the following buffer: 10 mM Tris-HCL, pH 7.4, 10 mM NaCL, 3 mM MgCl2, and 0.1% IGEPAL CA-630. Cells were transposed using a 1X concentration of Nextera Tn5 Transposase (Illumina) for 30 minutes at 37 °C with shaking at 500 rpm. Following transposition, DNA was purified using the MinElute PCR Purification Kit (Qiagen). DNA was amplified for 5 initial cycles using the custom Nextera barcoded PCR primers with the following parameters: 1 cycle of 72 °C for 5 minutes and 98 °C for 30 seconds, followed by 5 cycles of 98 °C for 10 seconds, 63 °C for 30 seconds, and 72 °C for 1 min. Following the initial 5 cycles of PCR, the additional number of cycles needed was determined by qPCR as previously described. Following the additional PCR cycles, DNA was obtained using the MinElute PCR Purification Kit and analyzed by Bioanalyzer (Agilent) prior to sequencing.