Extended Data Fig. 7: Spatial and temporal reconstruction of scRNA-seq data of the developing whisker HF epithelium.
a, b, t-SNE plot visualizing scRNA-seq data for 1,614 single cells from developing whisker HFs (E11.5, 94 cells; E12.0, 276 cells; E13.0, 267 cells; E13.5, 181 cells; E14.0, 177 cells; E15.0, 350 cells; and E17.0, 269 cells). Cell populations were categorized by embryonic stage (a) and cell type (b). c, Violin plot showing the expression patterns of known lineage markers in each cluster. Colours refer to t-SNE clusters in b. d, Subclustering of whisker HF epithelial cells identified in a–c. t-SNE plot of 962 epithelial cells is coloured by embryonic stage. e, Low batch effects and high reproducibility of scRNA-seq data; scRNA-seq samples in this study consisted of cells from multiple batches: a plurality of plates and different dates and places of sampling, library preparation and sequencing. To investigate the batch effect caused by this technical handling, transcriptomes were divided into stages and projected onto the t-SNE plot corresponding to d. Grey spots in the t-SNE plot indicate all transcriptomes derived from E11.5–E17.0 epithelial cells. Cells derived from each stage were highlighted with different colours according to the batch of experiments. Cells from different batches were mixed stage-by-stage on the t-SNE plot and not clustered by batch. This suggests the low batch effects and high reproducibility of our scRNA-seq analysis. f, t-SNE plot in d is coloured by cluster annotations. g, Percentage cell cluster distribution per individual plate. Each plate derived from the same embryonic stage showed a similar distribution of the clusters. h, Heat map of the heterogeneity within and between clusters. i, Dot plot showing differentially expressed genes in each cluster identified in f. j, Expression of cell-type-specific marker genes projected onto the t-SNE plot in d. k, Expression of the marker genes projected onto the t-SNE plot are shown in the top panels, and the corresponding RNA ISH results are shown in the bottom panels. Grey spots in the t-SNE plot indicate all transcriptomes derived from E11.5–E17.0 epithelial cells. Only cells derived from E17.0 are highlighted and coloured according to relative expression levels of the markers. Brackets indicate the intended localization of ISH signals. Scale bars, 100 μm.
