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. 2020 Nov 23;9:e60188. doi: 10.7554/eLife.60188

Figure 1. Single-cell sequencing of medullary thymic epithelial cells reveals population relationships.

(A) Outline of experimental design. Lineage relationships were first determined bionformatically from single-cell RNA-sequencing of control thymus. Lineage relationships and gene-expression events were then validated using both an inducible in vivo lineage tracing system and a model of transient thymus ablation and recovery. (B) UMAP visualization of all 2434 cells and clustering (color) of mTECs (two replicates, three pooled thymi each). Each point represents a cell. (C) Heatmap of genes curated from the literature across mTEC populations identified in this study. Color is mean-centered, log-normalized expression. Gene expression is the average expression within each mTEC population. (D) Normalized log expression of marker genes for known mTEC populations across cells in each cluster. Color represents cluster, black dot is median expression. (E) Single-cell velocity plot showing lineage relationships between mTECs projected onto a UMAP dimensional reduction. Arrows represent predicted developmental trajectories. See also Figure 1—figure supplement 1.

Figure 1.

Figure 1—figure supplement 1. Classification of medullary thymic epithelial cell populations.

Figure 1—figure supplement 1.

(A) Representative sorting strategy to isolate TECs. (B) UMAP dimensional reduction visualization of the thymic epithelial cells. Color represents original Seurat cluster. Some clusters were merged based on gene expression. Clusters 8 and 9 represent t-cells and were removed from the remainder of the analysis. (C) UMAP dimensional reduction visualization of the thymic epithelial cells. Color represents normalized log expression of marker genes for mTEC populations. Each point represents a cell. (D) Heatmap of all transcription factors and histone proteins differentially expressed between populations (adj-p-val<0.05 and log|fold change| > 2). High expression: yellow; low expression: blue. Aire interacting genes: red; knockout phenotype: blue. Cells organized by population, genes organized by hierarchical cluster.