Extended Data Fig. 3: Cell-type annotation for the epithelial lineage using UMAP plots. | Nature Genetics

Extended Data Fig. 3: Cell-type annotation for the epithelial lineage using UMAP plots.

From: Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis

Extended Data Fig. 3

a, Lineage-level UMAP for epithelial cells generated after final cell-type annotation. b, Select cell-type gene markers visualized in UMAP space across epithelial cells. c,e, UMAPs were additionally visualized for alveolar (c) and airway cell types (e) separately. Please note that KRT5−/KRT17+ cells were arbitrarily grouped with alveolar cell types, although they are found in PF in both remodeled airways and alveoli. d,f, Specific gene markers for alveolar (d) and airway cell types (f) visualized in UMAP space. For b, d and f, the specific cell types or groups of cells marked by each gene are listed near the gene name. ‘Transitional’ refers to general transitional epithelial marker genes, except where noted as a specific marker for only the transitional AT2 cell type.

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