Supplemental Figure 1 Developmentally regulated gene expression in WT NOD and B6 thymocytes. (A) Gene expression of tyrosine receptor kinase Epha2 is higher in NOD than B6 at all developmental stages. (B) Expression of Dapk1 is lower in NOD than B6 at all developmental stages, and off in NOD DN2a cells. Relative developmentally regulated expression in B6 subsets was confirmed using publicly available data from immgen.org. Supplemental Table 1. Genes differentially expressed >3X between NOD.Rag and B6.Rag CD25+DN thymocytes QTL or Log2 RPKM3 Gene Description congenic Chr Start Bp2 1 region B44 B7 N4 N7 Gm5828 predicted gene 5828 1 16,757,095 0.74 0.72 2.45 2.15 Efhc1 EF-hand domain (C-terminal) containing 1 1 20,941,707 0.94 1.01 0.13 0.13 Gm4956 predicted gene 4956 1 21,275,327 0.12 0.32 0.02 0.01 Khdc1a KH domain containing 1A 1 21,339,722 80.46 166.88 3.18 0.95 Khdc1c KH domain containing 1C 1 21,358,412 18.91 40.51 2.67 1.03 Khdc1b KH domain containing 1B 1 21,373,637 2.09 5.08 0.15 0.11 Gm8210 predicted pseudogene 8210 1 43,246,001 0.69 0.83 24.86 27.78 Gm8251 predicted gene 8251 1 44,112,797 0.12 0.24 0.06 0.03 Gm5527 predicted gene 5527 1 52,638,932 0.10 0.14 1.18 1.15 Ctla4 cytotoxic T-lymphocyte-associated protein 4 1 60,943,844 27.56 44.78 8.13 4.05 Obsl1 obscurin-like 1 1 75,475,885 0.21 0.01 0.76 0.58 Agfg1 ArfGAP with FG repeats 1 1 82,836,058 45.51 38.88 14.72 12.69 Gm7582 predicted gene 7582 1 85,024,529 0.08 0.12 0.89 1.42 A530032D15Rik RIKEN cDNA A530032D15Rik gene 1 85,084,714 0.50 0.91 2.66 3.2 Gm7609 predicted pseudogene 7609 1 85,196,188 0.09 0.15 0.96 1.61 Gm7592 predicted gene 7592 1 87,423,175 0.00 0 0.98 1.41 A630001G21Rik RIKEN cDNA A630001G21 gene 1 87,613,658 9.45 12.72 2.54 3.02 Rbm44 RNA binding motif protein 44 1 93,041,680 0.44 0.58 0.02 0 Per2 period homolog 2 (Drosophila) 1 93,312,559 0.39 0.22 1.08 0.84 Gpc1 glypican 1 1 94,728,263 1.42 1.3 4.42 4.95 Gm7889 predicted gene 7889 1 95,879,623 0.69 0.63 3.12 2.34 Ptprv protein tyrosine phosphatase, receptor type, N polypeptide 2 1 137,007,746 1.87 1.14 8.54 7.32 Rgs18 regulator of G-protein signaling 18 1 146,599,813 1.74 2.1 0.35 0.67 E330020D12Rik Riken cDNA E330020D12 gene 1 155,251,957 0.94 2.48 5.8 8.85 Tdrd5 tudor domain containing 5 1 158,185,426 2.04 2.4 0.49 0.34 Nphs2 nephrosis 2 homolog, podocin (human) 1 158,240,866 0.24 0.2 3.24 3.31 Rasal2 RAS protein activator like 2 1 159,070,665 0.09 0.14 0.47 0.56 Slamf1 signaling lymphocytic activation molecule family member 1 1 173,697,258 2.50 3.1 0.32 0.24 Igsf8 immunoglobulin superfamily, member 8 1 174,191,772 4.53 2.59 25.47 19.57 Gm4955 predicted gene 4955 1 175,398,640 3.45 3.53 0.41 0.38 Pyhin1 pyrin and HIN domain family, member 1 1 175,560,999 8.49 14.36 2.71 2.42 AI607873 expressed sequence AI607873 1 175,653,814 0.29 0.58 1.62 1.41 Ifi202b interferon activated gene 202B 1 175,892,706 0.00 0 49.65 43.41 Fmn2 formin 2 1 176,431,956 0.06 0.03 0.96 0.54 Sertad4 SERTA domain containing 4 1 194,670,625 0.06 0 0.49 1.44 Syt14 synaptotagmin XIV 1 194,723,501 0.37 0.57 1.37 1.54 Mnda myeloid cell nuclear differentiation antigen 1 175826486 2.09 2.59 7.68 7.31 Dpp7 dipeptidylpeptidase 7 2 25,207,796 2.15 2.19 10.85 10.11 Slc2a8 solute carrier family 2, (facilitated glucose transporter), member 8 2 32,828,510 0.46 0.18 1.34 1.44 Dab2ip disabled homolog 2 (Drosophila) interacting protein 2 35,413,786 0.28 0.12 0.94 1.22 Tanc1 tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1 2 59,450,099 0.15 0.15 1.18 1.77 Stk39 serine/threonine kinase 39, STE20/SPS1 homolog (yeast) 2 68,048,502 0.49 0.53 1.74 2.12 Itga6 integrin alpha 6 2 71,583,673 9.06 8.28 30.19 26.16 Rapgef4 Rap guanine nucleotide exchange factor (GEF) 4 2 71,819,297 0.42 0.38 1.98 1.56 Page 1 Supplemental Table 1. Genes differentially expressed >3X between NOD.Rag and B6.Rag CD25+DN thymocytes QTL or Log2 RPKM3 Gene Description congenic Chr Start Bp2 1 region B44 B7 N4 N7 Ctnnd1 catenin (cadherin associated protein), delta 1 2 84,440,228 2.57 1.61 6.25 6.16 Rpl30-ps3 ribosomal protein L30, pseudogene 1 2 90,587,773 2.00 4.26 10.98 15.49 Fjx1 four jointed box 1 (Drosophila) 2 102,289,523 0.23 0.09 0.48 1.35 Ryr3 ryanodine receptor 2, cardiac 2 112,471,512 0.00 0.03 0.08 0.16 Ltk leukocyte tyrosine kinase 2 119,577,056 0.00 0 1.9 1.37 Tyro3 TYRO3 protein tyrosine kinase 3 2 119,623,469 0.17 0.03 0.56 0.84 Mtap1a microtubule-associated protein 1 A 2 121,115,336 0.05 0.05 0.23 0.48 Gatm glycine amidinotransferase (L-arginine:glycine amidinotransferase) 2 122,420,203 0.02 0.08 1.36 1.53 AA467197 expressed sequence AA467197 2 122,462,722 2.88 7.11 37.64 31.71 Slc27a2 solute carrier family 27 (fatty acid transporter), member 2 2 126,378,143 1.54 0.96 0.15 0.14 Kcnip3 Kv channel interacting protein 3, calsenilin 2 127,282,234 1.05 1.03 0 0.02 Napb N-ethylmaleimide sensitive fusion protein attachment protein beta 2 148,519,721 0.43 0.65 2.87 2.95 Zfp345 zinc finger protein 345 2 150,296,727 0.16 0.21 0.83 0.92 Snph syntaphilin 2 151,416,285 0.01 0.04 3.59 2.58 Ttll9 tubulin tyrosine ligase-like family, member 9 2 152,788,221 1.89 1.57 0.16 0.12 BC020535 cDNA sequence BC020535 2 152,891,691 0.19 0.14 5.39 4.45 Hck hemopoietic cell kinase 2 152,934,204 0.18 0.23 2.38 1.28 Ahcy S-adenosylhomocysteine hydrolase 2 154,885,046 9.72 4.63 20.28 23.79 Atp9a ATPase, class II, type 9A 2 168,459,938 0.97 0.49 3.99 4.08 Gm9426 predicted gene 9426 2 169,443,209 3.54 3.81 0.06 0 Gm14403 predicted gene 14403 2 177,282,920 0.34 0.53 3.44 4.09 Col20a1 collagen, type XX, alpha 1 2 180,721,240 0.71 0.61 3.15 2.79 Tpd52 tumor protein D52 3 8,928,626 34.49 38.5 1.99 1.16 Zmat3 zinc finger matrin type 3 3 32,233,720 0.23 0.16 0.72 0.77 Gnb4 guanine nucleotide binding protein (G protein), beta 4 3 32,479,254 3.98 3.2 13.99 13.87 Fat4 FAT tumor suppressor homolog 4 (Drosophila) 3 38,785,862 0.24 0.16 0.01 0.02 E130311K13Rik RIKEN cDNA E130311K13 gene 3 63,718,606 0.63 0.86 3.27 2.72 Nes nestin 3 87,775,000 0.06 0 1.9 1.09 Tpm3 tropomyosin 3, gamma 3 89,876,571 73.76 53.8 9.76 11.67 Rplp0-ps1 ribosomal protein, large, P0, pseudogene 1 3 93,082,063 4.30 5.4 16.81 15.03 Tmod4 tropomodulin 4 3 94,928,398 0.40 0.57 5.14 4.73 Ptgfrn prostaglandin F2 receptor negative regulator 3 100,844,155 0.61 0.42 3.67 5.38 Igsf3 immunoglobulin superfamily, member 3 3 101,182,236 0.57 0.31 2.85 2.83 Slc22a15 solute carrier family 22 (organic anion/cation transporter), member 15 3 101,659,701 0.24 0.02 0.67 0.73 Fam102b family with sequence similarity 102, member B 3 108,773,915 3.40 3.14 13.14 16.3 Palmd palmdelphin 3 116,621,174 0.00 0 0.34 1.16 4930422G04Rik RIKEN cDNA 4930422G04 gene 3 127,256,407 2.95 3.16 10.84 9.33 Alpk1 alpha-kinase 1 3 127,373,317 1.27 1.96 6.87 6.79 Lphn2 latrophilin 2 3 148,478,550 0.31 0.24 0.02 0 Fam110b family with sequence similarity 110, member B 4 5,571,237 0.06 0.12 0.93 1 AI464131 expressed sequence AI464131 4 41,442,637 0.00 0.01 2.05 1.48 Cd72 CD72 antigen 4 43,459,334 0.91 1.41 0.16 0.18 Ptpn3 protein tyrosine phosphatase, non-receptor type 13 4 57,203,713 1.15 0.57 4.54 5.78 Akap2 A kinase (PRKA) anchor protein 2 4 57,730,529 3.76 3.62 13.54 12.21 Page 2 Supplemental Table 1.