Presence of self-antigen does not enhance secondary rearrangements. (A) Schematic representation of the predicted effects of deletion and TCR-editing scenarios on numbers of clonotype-positive and -negative thymocytes. (B) Expression of surface TCRβ and HYα on DP and CD8SP thymocytes from HY-STOP male and female BM chimeras. Representative results of at least five independent experiments are shown. (C) Absolute numbers (left) and percentage from total thymocytes (right) of TCRβ⁺HYα⁺ and TCRβ⁺HYα⁻ DP cells in male and female HY-STOP BM chimeras. **, P < 0.01; NS, not significant (P > 0.05); student’s t test; n = 5. Error bars represent the SD. Representative results of two independent experiments are shown. (D) Expression of Rag1 and Rag2 was analyzed by TaqMan qPCR in sorted TCRβ⁻ and TCRβ⁺HYα⁺ DP thymocytes from HY-STOP male and female BM chimeras. Mean relative expression normalized against Gapdh expression is shown. Error bars represent SD (individual mice; n = 4 for each group from two independent experiments). ***, P < 0.001; **, P < 0.01; student’s t test; NS, not significant (P > 0.05).