Fig. 2: Analysis of mesenchymal cells.

a, PAGA plot of the analysed 138,000 mesenchymal cells, from all 17 analysed donors, superimposed on their UMAP plot. Line thickness indicates the probability of the cluster connections. Colours indicate the 21 suggested clusters. ASM, airway smooth muscle; prol, proliferating; imm, immature; adv, adventitial; AF, airway fibroblast; fibro, fibroblast. b, Stereoscope analysis, based on ST data, showing the spatial distribution of the developing (1) mesothelial cells (cl-19), (2) pericytes (cl-14), (3) chondroblasts (cl-18), (4) ASM (cl-13), (5) AdvFs (cl-10) and (6) AFs (cl-16), in 6, 8.5 and 11.5 PCW lung sections. Red numbers: the highest percentage value of the indicated cell type. Dark red, high; grey, 0%. Tissue structure is shown by H&E staining. Scale bar, 400 µm. arw, airway; tr, trachea; prox, proximal; pcw, post conception week; br-v bundle, bronchovascular bundle. c, Pseudotime analysis of the ASM cells, with Slingshot showing the proliferation (cl-20) and maturation (cl-12 and cl-13) trajectories. Same colours as in a. d, As in b for the ASM trajectory, in a 6 PCW lung section. e, Spatial localization of the ASM and AF clusters, in a 6 PCW lung section, using probabilistic cell typing (pciSeq) with HybISS data. The pie charts show the percentage of the indicated cell identities. f, Representative image of one out of six distal epithelial bud tips for a 6 PCW whole lung section, showing the MYH11 (red), IGF1 (green) and COL13A1 (blue) detected mRNAs (HybISS) around the same airway, as in e. Data can be accessed at https://hdca-sweden.scilifelab.se/tissues-overview/lung/. g, Single-plane, confocal-microscopy image of immunofluorescence for COL13A1 (magenta), LUM (yellow) and ACTA2 (cyan), to show AFs and ASM, respectively, in an 8.5 PCW proximal airway (left). Square bracket indicates the area of the images on the right. Nuclear DAPI, grey. Scale bar, 20 µm.