GSM8075345: coD14_WT_ATAC_rep1; Homo sapiens; ATAC-seq
Day 14 cortical organoids (4x for each reaction) were harvested in 1ml DMEM/F12, and digested with Papain (20 units) for 6 minutes at 37°C. Organoids were dissociated into single cells, centrifuged at 300 RCF for 5 minutes, and counted in DPBS. Day 14 cortical organoids (4x for each reaction) were harvested in 1ml DMEM/F12, and digested with Papain (20 units) for 6 minutes at 37°C. Organoids were dissociated into single cells, centrifuged at 300 RCF for 5 minutes, and counted in DPBS.  ATAC-seq libraries were prepared according to the previously described Omni-ATAC protocol (Corces et al., 2017). In brief, 50,000 viable cells were pellet at 500 RCF at 4°C for 5 min, then resuspended in ATAC-seq resuspension buffer (RSB) (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1% NP-40,0.1% Tween-20 and 0.01% digitonin. Samples were incubated on ice for 3 min, then washed out with 1 ml RSB supplemented with 0.1% Tween-20. Nuclei were pelleted at 500g for 10 min at 4 °C. The nuclei pellet was resuspended in 50 μl transposition mix (25 μl 2× TD buffer, 5 μl transposase (TTE Mix V50, Vazyme # TD501), 16.5 μl PBS, 0.1 μl 5% digitonin, 0.5 μl 10% Tween-20, 3 μl H2O) and incubated at 37 °C for 30 min in a thermomixer with 1,000 rpm shaking. The reaction was cleaned up using VAHTS DNA Clean Beads (Vazyme # N411-01). Libraries were PCR-amplified using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme # TD501), usually for 10-12 cyles and purified with VAHTS DNA Clean Beads.