Fig. 8

Frequency scatter plots. a, c Frequency scatter plots among MHC-restricted TCRβ (a) and TCRα (c) repertoires from individual B6 mice. b, d Frequency scatter plots among MHCi TCRβ (b) and TCRα (d) repertoires from individual Quad^ko sequences. Each panel contains the comparison of three independent sequence repertoires from each strain of mice with the horizontal axis representing the frequencies of the first repertoire sequences, vertical axis representing the frequencies of the second (red circle) and third (green circle) repertoires. Common sequences between repertoire 1 and 2 are shown as red circles in the first quadrant with horizontal and vertical coordinates representing their respective frequencies in repertoire 1 and 2. Common sequences between repertoire 1 and 3 are shown as green circles with horizontal and vertical coordinates representing their respective frequencies in repertoire 1 and 3. Non-overlapping sequences appear on their respective axes. Top 200 common sequences present in all three repertoires are shown as filled yellow circles. Linear regressions of the frequency distributions between B6 repertoires 1 and 2 are shown in red lines. e CDR3β length-dependent expansion of MHCr and MHCi sequences from pre-selection repertoires. The percentage of expanded TCRβ sequences during thymic selection were plotted according to their CDR3 length for B6, Quad^ko and Quad^koBcl-2^tg. The analysis included common sequences between pre-selection (B6_DN) and MHCr (B6) or MHCi (Q and QB mice) repertoires. Expansion is defined as sequences whose mature frequencies (normalized for all comparing repertoires) were higher than their pre-selection ones. f Charged amino acid usages of CDR3β FG-loop in common sequences between pre-selection and MHCr or MHCi repertoires. B6 (+ 5%), top 5% TCRβ sequences of B6 repertoires; B6⁺, B6⁻, Q⁺, and Q⁻ represent mature sequences either expanded (+) or not expanded (−) in frequency compared to their pre-selection repertoire