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Figure S1. Comparable proportions and numbers of Treg in spleens of B6, NOD, R76 and R115 mice (A) Freshly isolated splenocytes from different mouse strains were analyzed by flow cytometry as shown for R76 mice. Upper plot show CD8 vs. CD4 expression on total splenocytes, lower plot Foxp3 vs. CD25 expression on CD4+ T cells electronically gated as depicted in upper plots. The proportion (B) and the number (C) of Foxp3+ Treg among CD4+ splenocytes of the different stains of mice was calculated using the gates indicated in Fig S1A (mean values ± SD, B6 n=5; NOD n=5; R76 n=4; R115 n= 4 mice; data pooled from two independent experiments). Using the Mann-Whitney test no statistical significance was found between the percentages and numbers of the stains analyzed.

Figure S2. Treg function and induction in NOD and R76 mice. (A) Effector and regulatory CD4+ T cells of NOD and R76 origin were purified and co-cultured at indicated ratios in the presence of anti- CD3∑ mAb and irradiated MHC° splenocytes for three days. Proliferation in these cultures was determined by measuring incorporation of 3H-thymidine. Shown is one experiment representative of three performed. (B) B6, NOD and R76 CD4+CD25- splenic T cells were cultured for four days in presence of TGF-® and plastic bound anti-CD3∑ and anti-CD28 mAbs. Cells were then analyzed by flow-cytometry for Foxp3 expression. (C) Results from four independent in vitro conversion assays performed as described in panel B. (D) Expression of CD122 by cells cultured as in panel B, determined by flow-cytometry.

Table S1. Comparison of the NOD and B6 coding sequences of 40 genes of the Trd1 locus.The sequences were downloaded from NCBI and sequence analysis was performed using MacVector. *The position and the nature of the mutations found, are shown, numbers indicate nucleotide position in coding sequence, “-“ indicates that no polymorphism was detected.

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