After crosslinking (1% (w/v) methanol-free formaldehyde 10 min RT 65 rpm), the reaction was quenched with 0.125 M glycine (5 min RT 65 rpm) followed by 30 min at 4 ºC. Organoid suspensions were collected on ice, centrifuged (3 min, 300 g at 4 ºC), washed with cold PBS, dissociated with 0.25% Trypsin-EDTA, and disaggregated for 3 min. Cells were centrifuged, washed, flash-frozen, and stored at -80 ºC. Cells were lysed overnight at 37 ºC 300 rpm and chromatin digested. Biotinylated DNA from the Hi-C was selected using Dynabeads MyOne Streptavidin T1 beads from ThermoFisher Scientific. Hi-C libraries were prepared using the NEBnext End Repair Module, NEBNext dA-Tailing Module and NEBnext Quick Ligation Reaction Buffer(5X) from New England Biolabs, complemented with NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) from New England Biolabs. 1µg of DNA was used as starting material. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected at 100-600bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent 4150 TapeStation system (D5000 ScreenTape).