Cell types in GSE132771 (Sheppard-UCSF single cell cohort) [19].

Clustering was performed using R package Seurat and cell types were identified using known markers. A. Total lung cell suspension. SPP1_monocytes_0: SPP1+ monocytes; Infl_monocytes_1: Inflammatory monocytes; ACKR1pos_endo_2: ACKR1+ endothelial cells; ACKR1neg_endo_3: ACKR1- endothelial cells; Fibroblasts_4: Fibroblasts; AT2_5 and AT2_23: Alveolar epithelial cell type II subpopulations; Th_6: helper T cells; Pericytes_7 and Pericytes_22: Pericyte subpopulations; HLAhigh_mac_8 and HLAhigh_mac_10: HLA class II high macrophage subpopulations; Sm_9: smooth muscle cells; Bcells_11 and Bcells_21: B cell subpopulations; Tc_12: cytotoxic T cells; AT1_13: Alveolar epithelial cell type I; PC_14: Plasma cells; Endo_15 and Endo_24: endothelial cell subpopulations; Ciliated_16: ciliated epithelial cells; Monocytes_17 and Monocytes_18: Monocyte subpopulations. B. Lineage sorted cells. THY1high_alv_fib_0: THY1 high alveolar fibroblasts; THY1pos_sm_1: THY1+ smooth muscle; THY1neg_sm_2: THY1- smooth muscle; CTHRC1pos_3: CTHRC1+ fibroblasts; Adventitial_4: Adventitial fibroblasts; THY1neg_alv_fib_5: THY1- alveolar fibroblasts; Pericytes_6: Pericytes; Peribronchial_7: Peribronchial fibroblasts; Sm_8 and Sm_13: smooth muscle cell subpopulations; Alveolar_9 and Alveolar_10: Alveolar fibroblast subpopulations; Epi_11: Epithelial cells; Hematopoietic_12 and Hematopoietic_14: Hematopoietic cells. C. Heatmap (left panel) and correlation matrix (right panel) in GSE47460 of genes included in the signature derived from the ‘Total lung cell suspension’ (shown in panel A) dataset across each cluster shown in panel A. D. Heatmap (left panel) and correlation matrix (right panel) in GSE47460 of genes included in the signature derived from the ‘Lineage sorted’ (shown in panel B) dataset across each cluster shown in panel B. (ZIP)