Extended Data Fig. 8: In vivo expression patterns of representative genes in each cell cluster of E13.0–E17.0 whisker HFs.

Feature plots of characteristic differentially expressed genes in each cluster identified in Extended Data Fig. 7f are shown in the left panels. Feature plots divided by developmental stages of the whisker HFs (E13.0–E17.0) and the corresponding RNA ISH images are shown on the top and bottom right panels, respectively. Grey spots in the t-SNE plot indicate all transcriptomes derived from E11.5–E17.0 epithelial cells. Only cells derived from the indicated stage are highlighted and coloured according to relative expression levels of the indicated markers. Arrowheads indicate the intended localization of ISH signals. A cell cluster located at the lower part of the t-SNE plot (clusters 5 and 6) corresponded to the upper part of the HF, such as the infundibulum and junctional zone. A bulge SC marker (Nfatc1) was strongly expressed in cell clusters 7–12 located in the centre of the t-SNE plot. These clusters were divided into the upper and lower bulge regions, based on the expression pattern of each region marker (such as Adamts20 and Shisa2). Vdr expression confirmed that clusters 7, 11 and 13 contained cells derived from the stalk region, the lower part of the HF. Shh-positive cells in cluster 14 were in the hair germ in vivo. These data indicated that cells were aligned from the bottom left to the top right on the t-SNE plot, reflecting the tissue architecture of the whisker HF. Scale bars, 100 μm.