a, Overview of the pan-tissue single-cell transcriptomic atlas. Created in BioRender; Shi, Q. (2025), https://BioRender.com/g2chn78. b, UMAP visualization of total cells (dots) coloured by tissue (top) or cell type (bottom). Tissue colours match those in a. c, Cell-type composition across tissues. Cell-type colours match those in b. Only sorting-free samples are included. d, Unsupervised hierarchical clustering of 76 non-epithelial cell subsets coloured by cell type. ABC, age-associated B cells; Bm, memory B cells; Bn, naive B cells; cDC, conventional dendritic cells; CMC, cardiac muscle cells; DC, dendritic cells; Fb, fibroblasts; GCB, germinal centre B cells; gdT, γδ T cells; immNeu, immature neutrophils; MAIT, mucosal-associated invariant T cells; mNeu, mature neutrophils; Mo, monocytes; Mph, macrophages; pDC, plasmacytoid dendritic cells; SkMC, skeletal muscle cells; SMC, smooth muscle cells; Tem, effector memory T cells; Temra, terminally differentiated effector memory or effector T cells; Tfh, follicular helper T cells; Tm, memory T cells; Tn, naive T cells; Treg, regulatory T cells; Trm, tissue-resident memory T cells. e, Tissue prevalence of fibroblast subsets measured by Ro/e (the ratio of observed to expected cell numbers) (Methods). Tissues are categorized and ordered by body system. Fibroblast subsets are ordered by Shannon equitability from most universal (S01) to most specialized (S12). f, Spatial distribution of fibroblast subsets across tissues (Visium). Relative frequencies of each fibroblast subset among total fibroblasts are shown for individual spots.
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