Extended Data Fig. 1: scRNA-seq analysis of CD45⁻ cells in lymph nodes.

a, UMAP plot of 5,470 stromal cells (dots) from lymph nodes of 10 mice colored by cluster (top) and split by replicate (bottom). b, Left: Projection as in a) colored by expression of indicated genes. Right: Heatmap of the 50 most strongly upregulated genes (rows) in cells from each of the 3 main cell populations (columns): Blood endothelial cells [BECs], lymph node endothelial cells [LECs] and fibroblasts. c, Left: Heatmap of the 10 most strongly upregulated genes (rows) for each LEC subpopulation compared to all other LEC cells (columns). Right: Heatmap of the 10 most cluster-specific genes for each BEC subpopulation compared to all other BECs. d, UMAP plot of fibroblastic cells from Fig. 1a colored by the expression of indicated marker genes. e, Heatmap as described in (c), here of the 10 most cluster-specific genes for each Cd34⁺ fibroblast subpopulation from Fig. 1a compared to all other Cd34⁺ fibroblasts. f, Heatmap as described in (c), here of the most strongly enriched genes for fibroblast subpopulations from Fig. 1a. For all heatmaps most strongly enriched genes were defined as the genes with largest LogFC compared to all other cells in the dataset; at most 10 genes are shown per cluster, but less if one or more genes were not uniquely enriched in just the cluster under consideration.