library_construction_protocol: AEC-ON cells grown in 2D and 3D were processed in parallel. Cells grown to about 80% confluence in 2D were detached with Accutase at room temperature, collected in growth media, centrifuged, resuspended, and counted manually using a hemacytometer. In parallel, AEC-ON organoids were released from Matrigel in three rounds of Dispase treatment at 37°C followed by centrifugation. The initial release of organoids and subsequent disaggregation into a single-cell suspension was monitored by visual inspection. The final single-cell suspension was then counted manually with a hemacytometer. Both 2D and 3D cell suspensions were FACS sorted for GFP+ SV40 LgT-transduced epithelial cells. Samples were then prepared as recommended by the 10x Genomics user manual. Libraries were constructed according to recommended user guidelines for the 10x Genomics Chromium Single Cell 3' GEM, Library, & Bead kit v3 (PN-1000092).