Extended Data Fig. 8. Clonal deletion gating strategy.

Flow cytometry gating strategy for identifying thymocytes undergoing clonal deletion or death by neglect. Signaled and non-signaled cells were identified based on expression of CD5 and TCRβ (middle, left; green gate (signaled), gray gate (non-signaled). Thymocytes undergoing death by neglect were identified from non-signaled cells based on expression of cleaved caspase-3 (bottom, left; gray gate). Cortical and medullary thymocytes were identified based on expression of CCR7 (middle, middle). Medullary CD4 thymocytes undergoing clonal deletion were identified from signaled CCR7⁺ CD4⁺ cells based on expression of cleaved caspase-3⁺ (bottom, right; red gate). Numbers adjacent to outlined areas represent percent cells in each.