At indicated time points, organoids were randomly sampled into ice-cold 1X PBS solution and subsequently fixed in 4% paraformaldehyde (PFA) solution in 1X PBS overnight at 4 °C with gentle agitation. After several 10 min washes in 1X PBS, organoids were immersed overnight in 30% sucrose in 1X PBS and embedded in Tissue-Tek 4566 cryomolds (Thermo Fisher, # 10844231) using optimal cutting temperature (OCT) embedding matrix (Carl Roth, #6478). Cryomolds were placed on dry ice and fixed frozen tissue blocks were stored at − 20 °C before sectioning. Tissue blocks were sectioned at 20–30 µm thickness onto SuperFrost Plus microscope slides (Fisher Scientific, #J1810AMNZ) using a CryoStar NX70 (Thermo Fisher) cryostat.
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