Extended Data Fig. 6: Cell sorting of photo-converted developing whisker HF epithelial cells.

a, Photo-labelling of whisker HF epithelial cells in nKikGR mice at each embryonic stage. Scale bars, 50 μm. b, Single plane of E15.0 whisker HF showing the nKikGR signal intensities before and after the photo-conversion (Supplementary Video 9). Expression level of nKikGR varies between cells. There are two possible reasons for this: (1) the expression level of nKikGR varies for different cell types, and (2) the different mesenchymal tissue thickness of the explants around the whisker HFs affects the efficiency of detecting the fluorescent signals from the inside of the tissue. Despite this, the variation of nKikGR-green signal levels within the HF before photo-conversion closely correlates with the variation of nKikGR-red signal levels after photo-conversion, suggesting that the nKikGR signal was completely converted from green to red throughout the HF tissues (Supplementary Video 9). Scale bars, 50 μm. c, Experimental design for scRNA-seq of the developing whisker HF epithelium. d, Immunofluorescence staining of E14.0 whisker HF showed that the basal epithelial layer was marked by ITGA6⁺CD31⁻ and that blood vessels in the mesenchyme were labelled by ITGA6⁺CD31⁺ (arrowhead). Box shows magnified region (right). Scale bars, 50 μm. e–g, Isolation of photo-labelled whisker HF epithelial cells (E12.0–E17.0, DAPI⁻CD31⁻ITGA6⁺KikGR-red⁺ cells; E11.5, DAPI⁻CD31⁻ITGA6⁺ cells) by flow cytometry. h–l, Immunolocalization of ITGA6 in developing whisker HFs. Whisker HFs at E12.0 (h), E13.0 (i), E14.0 (j), E15.0 (k) and E17.0 (l) were stained with an antibody against ITGA6, and sections were counterstained with DAPI. ITGA6 was detected in all basal epithelial cells of developing whisker HFs. Blood vessels in the dermis also were positive for ITGA6. Scale bars, 100 μm.