Altered TCR repertoire selection in Shh mutant thymus. (A) Thymus phenotype of 4-week-old Shh+/\#8722; HY-TCR female mice. CD4 and CD8 profiles of HY-TCR and Shh+/\#8722; HY-TCR littermate mice (left dot plots). Mean thymus sizes were 3.7 × 107 for HY-TCR and 4.8 × 107 for Shh+/\#8722; HY-TCR. CD4 and CD8 profiles gated on DbSmcy-positive cells in the HY-TCR and Shh+/\#8722; HY-TCR thymus (right dot plots). (B) Thymus phenotype of E17.5 Shh\#8722;/\#8722; HY-TCR female FTOC cultured for 10 days. CD4 and CD8 profiles of HY-TCR and Shh\#8722;/\#8722; HY-TCR littermate FTOC. Bar chart shows the relative percentage of transgenic (Tg) TCR+ CD8bright SP cells for HY-TCR (n = 3) and Shh\#8722;/\#8722; HY-TCR (n = 3); P = .027. The histograms show V\#946;8 and T3.70 (transgenic TCR\#945; chain) staining on CD8SP cells. (C) Thymus phenotype of 12-day-old Shh+/\#8722; HY-TCR male. CD4 and CD8 profiles of HY-TCR and Shh+/\#8722; HY-TCR littermates. Mean thymus sizes were 2.4 × 107 for HY-TCR and 2.1 × 107 for Shh+/\#8722; HY-TCR. Bar charts show the relative percentage of transgenic (Tg) TCR+ CD8bright SP or DP cells for HY-TCR (n = 3) and Shh+/\#8722; HY-TCR (n = 3); P = .019. The histograms show V\#946;8 and T3.70 expression on CD8SP cells. (D) Thymus phenotype of E19 Shh\#8722;/\#8722; HY-TCR male. CD4 and CD8 profiles of HY-TCR, Shh+/\#8722; HY-TCR, and Shh\#8722;/\#8722; HY-TCR littermates. Mean thymus sizes were 2.5 × 105 for HY-TCR, 2.4 × 105 for Shh+/\#8722; HY-TCR, and 1.1 × 104 for Shh\#8722;/\#8722; HY-TCR. Bar charts show the relative percentage of Tg TCR+ CD8bright SP or DP cells for HY-TCR (n = 4), Shh+/\#8722; HY-TCR (n = 4, P = .034), and Shh\#8722;/\#8722; HY-TCR (n = 3, P = .018). The histograms show DbSmcy and T3.70 staining on CD8SP cells. Numbers in dot plots indicate the percentage of cells falling in the quadrant. Error bars show SE. Data are representative of at least 3 experiments.