SRA

The scRNA-seq data are an integral part of the manuscript with the above title. Using a photo-labelling technique and RamDA-seq as described in the overall design, we obtained accurate scRNA-seq data from developing hair follicles (HFs), reflecting the spatiotemporal dynamics of cellular state transition during HF morphogenesis. Single cell transcriptome analysis identified cell types, which cannot be distinguished by known makers, their signature markers, and transcriptional state changes in developing HFs. By integration of the data from single cell live imaging, our findings revealed the origin and developmental trajectories of tissue stem cells (SCs), leading to a new model of HF development and SC induction with unprecedented resolution. Overall design: Embryonic skin tissues contain a mix of different HF types at different developmental stages, rendering separation and transcriptional profiling of HFs at specific developmental stages difficult. We thus developed a transgenic mouse line expressing a photo-convertible fluorescent protein, nuclear Kikume Green-Red, which enables identification and photo-labelling of target HFs under a confocal microscope. Entire single whisker HFs at E12.0, E13.0, E13.5, E14.0, E15.0, and E17.0 were photo-converted. Basal epidermal cells of each photo-labelled HF (E12.0–E17.0, ITGA6+/CD31-/kikGR-red+ cells; E11.5, ITGA6+/CD31- cells) were isolated as single cells by FACS. All scRNA-seq libraries were constructed for RamDA-seq, a novel sensitive and accurate total scRNA-seq method. We obtained single cell full-length total RNA sequencing of developing whisker HFs as follows: E11.5, 94 cells; E12.0, 280 cells; E13.0, 276 cells; E13.5, 189 cells; E14.0, 183 cells; E15.0, 362 cells; E17.0, 282 cells (total: 1,666 single cells). Please note that total 1,666 samples were included in the data analysis, however, the processed data file contains only 1614 data columns due to low-quality samples (indicated as the sample 'characteristics: data quality = low').