GSM8698489: tKO_2_pluri_ATAC; Homo sapiens; ATAC-seq
hPSC derived WT and ETV1 KO PP spheroids, were dispersed with Tripsin, washed with 0.1% saponin – 1% BSA – PBS, filtered through 30 μm mesh filter. Afterwards cells were counted using Countess and adjusted to 700-1,200 cells/μl. The scRNA-seq was performed with 10xGenomics platform and Illumina according to the manufacturer's protocol. Libraires were pair-end sequenced with depth of 40,000 reads per cell. ATAC-seq: The WT, KO and tKO hPSCs or PPs were dispersed to single cells using TrypLE. The 5 x 104 cells were resuspended in 50 µl of cold ATAC-RSB buffer (10mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2,, 0.1% Tween-20, 0.1% NP-40). For nuclei extraction, the cells were incubated with 0.1% digitonin for 3 min at 4 °C and centrifuged at 500 x g for 10 min at 4 °C with the addition of 1 ml ATAC-RSB. The supernatant was discarded, and nuclei were prepared for the transposition reaction. The solution containing transposed fragments was purified using the Zymo DNA Clean & Concentrator (Zymo Research, USA) and the transposed DNA was eluted in 20 μl H2O and stored in -20 °C. Barcoded adapters were added to the transposed fragments by PCR with the NEBNext Ultra II Q5 2x Master Mix (New England Biolabs, USA), according to the producer protocol and after purified with the AMPure XP beads. The samples were 150 bp paired-end sequenced on the NovaSeqX platform.