Extended Data Fig. 3: Identification of the origin and lineage dynamics of HF epithelial cells by long-term live imaging.

a, Schema of epithelial cell subpopulations at the hair germ stage, which we defined for cell tracking. Magenta, IFE basal cells; red, basal cells located in the upper half of the HF; yellow, basal cells located in the lower half of the HF; blue, cells adjacent to the dermal papilla; green, suprabasal cells in the IFE or HF. b, Lineage tree reconstructed from tracking of a hair germ cell and its progeny. The x axis shows the duration of imaging. Lineage is colour-coded based on cell fate, and cell fate was identified based on the cell position in tissue. Scale bars, 50 μm. c, Examples of lineage trees of tracked upper, lower and hair germ cells in Fig. 1a. d, e, HF development is accomplished by enlarging each earlier compartment longitudinally aligned in the follicle epithelium. Data of replicate whisker HFs related to Fig. 1a, b are shown. d, Snapshot images (top panels) and lineage tracking data (bottom panels) of long-term continuous imaging of whisker HF development from the hair germ to bulbous peg stage. Different epithelial lineages were longitudinally aligned as 3D cylindrical compartments in HFs, and prospective bulge SCs were located in the upper part of the HF as shown in Fig. 1a (replicate no. 1, represented in the main figure). Scale bars, 100 μm. e, Cell fates of epithelial cells in the IFE, upper, lower, hair germ and inner regions of the hair germ stage. Cell fates at the bulbous peg stage are shown. f, Bar plot converted from stacked bar plot of Fig. 1b. Statistical analysis was performed by one-way ANOVA followed by Tukey’s test. g–i, Different epithelial lineages are aligned in a concentric manner in the placode. Replicate whisker HFs related to Fig. 1c–e are shown in g–i. g, Snapshot images (top panels) and lineage tracking data (bottom panels) of long-term continuous imaging of whisker HF development from the placode stage to hair germ stage. Origin of prospective bulge SCs (red) was located at the periphery of the hair placode as shown in Fig. 1c (replicate no. 1, represented in the main figure). Scale bars, 50 μm. h, Bee swarm plot showing the distances of cells from the placode centre. Different epithelial lineages were aligned in a concentric manner in the placode. Statistical analysis was performed by two-sided unpaired t-test. i, Fate of basal and suprabasal cells of the hair placode stage. Cell fates at the hair germ stage are shown. j, Summary of the developmental origins and lineage dynamics of HF epithelial cells. The embryonic stage at which imaging started is indicated in each figure. Each value in the graph is the mean ± s.d. from three independent experiments, one HF each. Numbers of analysed cell lineages are summarized in Supplementary Table 1. See also ‘Statistical analysis and reproducibility’ in Methods and Source Data.