Fig. 2: Organ cell types and gradients.
From: A molecular cell atlas of mouse lemur, an emerging model primate
a, Dendrogram of 71 identified kidney molecular types. b, Left, UMAP of kidney epithelial cells (L4, 10x). The trajectory (black line, cell density ridge) corresponds to the known cell spatial continuum along the nephron, beginning with the proximal convoluted tubule (55) and ending with the principal cells of the collecting duct (64–66). Note that macula densa cells (62) cluster between thin (58–59) and thick (60) ascending loop of Henle cell types and urothelial cells (69) near the principal cells of the collecting duct. Intercalated cells of the collecting duct (67–68) and podocytes (54) lie off the trajectory. Dots, individual cells coloured by molecular type; thin grey lines, cell alignments to the trajectory. Right, heatmap showing the relative expression of nephron markers along the trajectory ((ln[UP10K + 1] normalized for each gene to its maximal value (99.5 percentile) along the trajectory). Coloured bar, cell-type designations (as for the UMAP). c, Left, UMAP of vasa recta endothelial cells (L4 kidney, 10x). The trajectory reflects the spatial cell continuum along the vasa recta descending limb (VR D, 79–80) and the ascending limb (VR A, 81–82). Right, heatmap showing the relative expression of vasa recta markers along the trajectory. Note the marker transition from artery–arteriole (GJA5+) to capillary (CA4+) to vein (ACKR1+). d, Top, UMAP of male germ cells (L4 testis, 10x) corresponding to the spermatogenesis trajectory from stem cells (spermatogonia, 250) to late spermatids (256). Bottom, heatmap showing the relative expression of spermatogenesis markers along the trajectory (spermatogonium panel enlarged for resolution). e, Top left, UMAP of myeloid cells (L2 bone, bone marrow, 10x) corresponding to two haematopoiesis trajectories. One begins with haematopoietic precursor cells (169) and bifurcates at granulocyte–monocyte progenitors (181) into the neutrophil lineage (175–176) and the monocyte–macrophage lineage (182–184 and 187). The other connects erythroid progenitor and lineage cells (172–174) with a fraction of megakaryocyte progenitors nearby (170). Top right and bottom, heatmaps showing the relative expression of haematopoiesis markers along trajectories (neutrophils uniformly subsampled). Symbols in brackets indicate the description of genes identified by NCBI as loci: [DMC1], LOC105858542; [HSPA1L], LOC105858168; [CD14], LOC105862649; [HBB], LOC105883507; and [HBA2], LOC105856254. See also Extended Data Fig. 2.
