Fig. 1
Single-cell transcriptomics reveal thymic differentiation pathway of IELPs. a t-distributed stochastic neighbor embedding (t-SNE) map representation of transcriptome similarities between 645 cells of 4-week-old TBGR mouse clustered by RaceID3 (left). Bar diagram showing the cumulative percentage of the sample contribution, normalized by sample size, to each cluster (mid). t-SNE map showing the sample information for RaceID3 clustered cells with an overlaid putative differentiation trajectory derived by StemID2 (right). b Self-organizing map (SOM) of z-score transformed pseudo-temporal expression profiles, grouped into 10 modules of co-expressed genes, along the putative differentiation trajectory (5→3→1→4→2). The pseudo-temporal order was inferred by StemID2-derived projection coordinates of all cells. The color codes below the SOM indicate the cluster information (upper panel) or sample information (lower panel). c–e Example expression profiles of the SOM-identified modules representing confirmed agonist-selection markers Id2 (encodes for Id2) (c), Ikzf2 (encodes for Helios) (d), and Nr4a1 (encodes for Nur77) (e) along the predicted IELP differentiation trajectory from b with cluster information (left panel) and sample information (right panel). The black line in each plot indicates a local regression. f Correlation of agonist-selection markers Helios and Nur77 was also observed on protein level as shown by flow cytometric analysis of NK1.1− IELPs from 6- to 12-week-old TBGR mice. Numbers denote the percentage of cells in the gate (Mean ± SEM) from three mice, experiments were performed twice, and one representative result is shown. g, h Expression profiles of Pdcd1 (encodes for PD-1) (g) and Id3 (encodes for Id3) (h) along the predicted IELP differentiation trajectory from b with cluster information (left panel) and sample information (right panel). The black line in each plot indicates local regression
