GSM9021708: HEK, SLX4IP, HU treated, Biol. RepB, techn. Rep2; Homo sapiens; OTHER
Nuclei isolation from in vitro cultured cells. For nuclei isolation, HEK cells were incubated in NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1 % Triton X-100, 20 % glycerol, 1X cOmplete Proteinase Inhibitor) for 5 min on ice. U2OS cells were incubated in NE1 buffer for 20 min on ice. Nuclei were fixed with 0.1 % formaldehyde (Thermo Scientific, 28906) in PBS for 2 min at room temperature. Formaldehyde was quenched with 75 mM glycine and nuclei were pelleted by centrifugation at 1,300 xg for 4 min at 4 °C. Purification of the tagmented DNA fragments was performed using the Zymo DNA Clean and Concentrator kit (D4033, Zymo Research). DNA was eluted in 23 µL nuclease-free water and as previously described (https://www.nature.com/articles/s41467-019-09982-5). Optimal number of cycles was determined via qPCR as previously described. Amplified sequencing libraries were subjected to double sided size-selection (right side: 0.65X, left side: 1.3X) using SPRI beads followed by elution in 23 µL nuclease-free water.