human foetal lung organoids:  For testing transduction efficiency, organoids were dissociated into single cells using pre-warmed TrypLE Express (12605028, Thermo Fisher Scientific) at 37°C for 10 min. The reaction was terminated by adding Advanced DMEM/F12 (12634028, Thermo Fisher Scientific) and cells passed through a 30 µm cell strainer. 2 . 105 organoid single cells were re-suspended with Lonza P3 nucleofectionbuffer and 1 µl of pmaxGFP (Lonza) and transferred to 20 µl nucleofection cuvette (V4XP-3024, Lonza). Nucleofection was performed using Lonza 4D Nucleofector with X unit using the program EA125. After nucleofection, self-renewing medium supplemented with 10 µM Y-27632 (ROCK inhibitor, ROCKi, 688000, Merck) was added to dilute the P3 buffer. Cell mixture was then seeded in Matrigel in two wells of a 24-well plate and cultured with self-renewing medium with ROCKi (10 µM) for 72 hr before FACS analysis.

human foetal intestinal organoids: For gene targeting, 3 µl spCas9 (4 µg/µl) and 4.32 µl of SOX9 ssRNA (100 µM, Synthego) were mixed and incubated at RT for a minimum of 10 min in order to form ssRNPs. At the same time, human foetal intestinal organoids were dissociated into single cells, according to the protocol previously described for nucleofection. 6 . 105 cells were suspended using Lonza Nucleofection P3 buffer, mixed with 6 µg of SOX9 reporter repair template plasmid. The cell suspension was further mixed with pre-formed Cas9 RNPs and equally distributed into three 20 µl cuvettes. Nucleofection was performed using the program EA125 for human intestinal lung organoids. After nucleofection, intestinal organoid maintenance medium with ROCKi was added to dilute the P3 buffer. The cell mixture was then taken out and seeded in Matrigel in six wells of a 24-well plate and cultured with maintenance medium with 10 µM ROCKi for 1 week before flow cytometry.