For cell culturing, unsorted P0 and P7 CGNPs were resuspended in culture media (DMEM-F12 (Gibco, New York, NY, USA) supplemented with 1% N2 (Invitrogen, Waltham, MS, USA); 1.5% glucose (Invitrogen); 5 μM HEPES (Invitrogen); and 0.25 μg/mL SHH (R&D Systems, Minneapolis, MN, USA)). The cells were seeded on pre-coated plates with poly-D-lysine (100 μg/mL, Sigma) at a density of 250.000 cells per well in 24-well plates. For ionizing radiation experiments, the cells were irradiated the next morning with 0.5, 1 or 2 Gray of Y-rays from a 137Cesium source (IBL 637 Cesium-137 Y-ray-machine). The cells were fixed at 2 h post irradiation. For reversine treatment, the cells were treated with DMSO or 250 nM of reversine (Sigma) for 48 h and subsequently fixed.
For gDNA, RNA, and protein isolations, tdTomato positive/DAPI negative cells were sorted on a Beckman Coulter MoFlo Astrios sorter (Brea, CA, USA). Cell pellets were stored at −80 °C until further processing. For the isolation of nuclei for scWGS, see below.