library_construction_protocol: For isolation of lung cell, mice were culled by cervical dislocation and lungs cleared of blood via perfusion with 10ml of PBS. Lungs were inflated with 2-3ml of a Dispase solution via intratracheal injection. When isolating mesenchymal cells, Collagenase I was added to the Dispase solution at 350U/ml before inflation. Lungs were carefully dissected out of the thoracic cavity and placed on a petri dish on ice. Individual lobes were separated from each lung, placed in a 50ml falcon and minced into small pieces. Cells were washes down with 3ml of PBS to the bottom of the falcon tube. When isolating epithelial cells only, 60ul of 100mg/ml Collagenase/Dispase solution was added per tube. Samples were places in a shaking incubator at 37ºC, 190 rpm, for 45 min. 7.5ul of 1% DNase I was added to each sample in the final 10 min of incubation. The resulting cell suspensions were filtered sequentially through 100 µm and 40 µm cell strainers and washed with 2 ml of 10% foetal bovine serum (FBS) in PBS (PF10) to collect remaining cells. Samples were centrifuged at 800 rpm for 5 min at 4ºC. Supernatant was removed and pellets were resuspended in 1 ml of red blood cell lysis buffer (RBC buffer, made inhouse: 150 mM NH4Cl and 10 mM KHCO3 in distilled H2O) for 60 seconds at RT. After lysis, 6 ml of Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 820 (DMEM/F-12) was added to the tube to neutralize the RBC buffer. 500µL of filtered FBS was added slowly to the bottom of each tube to collect live cells. Tubes were centrifuged again at 800rpm for 5 min at 4ºC. Cell pellets were resuspended in PF10 and placed into separate 1.5 ml tubes for antibody staining. Lineage-labelled epithelial cells (EpCAM+RFP+) and a mixed population of mesenchymal and immune cells (1:1 ratio of mesenchymal cells (CD45–CD31–EpCAM–) and immune cells (CD45+CD31–EpCAM–)) were then sorted and submitted for sequencing. Cell suspensions were spun down, counted, and resuspended in 0.04% bovine serum albumin (BSA) in PBS to achieve a cell concentration of ~345 cells/µL. Single-cell 3′ RNA-seq libraries were generated according to manufacturer's instructions (Chromium Single Cell 3′ Reagent v3 Chemistry Kit, 10X Genomics) and cDNA quality was assessed.