Supplementary Figure 1: Gating strategy for thymic epithelial cells and dendritic cells.

(a) Contour plots depicting the initial gating strategy for analysis of eGFP and eYFP expression by EpCAM⁺ thymic epithelial cells and dendritic cells. Briefly, thymuses were enzymatically digested to produce single cell suspensions, which were enriched for EpCAM⁺ and CD11c⁺ cells. Doublets were excluded. Numbers indicate the percent of cells in each gate.

(b) Contour plots showing the gating strategy for EpCAM⁺ thymic epithelial cells, proceeding from singlet gate 2 (a). EpCAM⁺ CD45.2⁻ stromal cells were gated for further analysis by excluding CD90.2⁺ T cells, dead cells, CD19⁺ B cells, macrophages and dendritic cells (CD11b⁺ and CD11c⁺). Remaining cells were analyzed further in Figure 7. Numbers indicate the percent of cells in the gate.

(c) Contour plots showing the gating strategy for thymic dendritic cells, proceeding from singlet gate 2 (a). CD11c⁺ cells were gated and dead cells, CD90.2⁺ T cells, CD11c^hiCD11b^hi eosinophils, CD19⁺ B cells, and autofluorescent macrophages (shaded, blue gate) were then excluded. Remaining CD11c⁺CD11b^lo–int cells were analyzed further in Figure 7. Numbers indicate the percent of cells carried forward for analysis.