GSM7061471: CD34 cells, SF3B1-mutant MDS, replicate 3, ATAC-seq; Homo sapiens; ATAC-seq
50,000 K562 cells or 5000 CD34+/murine HSC cells (flow sorted) were harvested, washed, and resuspended in PBS. Washed cells were resuspended in ATAC-seq resuspension buffer and  centrifuged at 500g for 5 min in a 4 °C. Cell pellets were then resuspended in 50 μl of ATAC resuspension buffer. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500g at 4 °C. Supernatant was carefully removed and nuclei were resuspended in transposition mix containing transposase enzyme by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 rpm. DNA quality and size distribution were checked on Fragment Analyzer. 10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit