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. 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 Hdhd3 haloacid dehalogenase-like hydrolase domain containing 3 4 62,160,042 0.56 0.61 2.62 2.26 Alad aminolevulinate, delta-, dehydratase 4 62,170,203 8.69 6.35 25.88 25.88 Orm2 orosomucoid 2 4 63,023,483 0.24 0.43 2.32 2.74 Dock7 dedicator of cytokinesis 7 4 98,603,366 0.28 0.2 1.01 1.12 Echdc2 enoyl Coenzyme A hydratase domain containing 2 4 107,838,042 0.40 0.15 3.25 2.03 Heyl hairy/enhancer-of-split related with YRPW motif-like Congenic? 4 122,910,799 1.91 1.08 4.82 7.98 Ndufs5 NADH dehydrogenase (ubiquinone) Fe-S protein 5 Congenic 4 123,389,953 34.62 30.31 8.41 7.99 Ubxn11 UBX domain protein 11 Congenic 4 133,658,485 1.63 1.33 4.28 4.64 Padi3 peptidyl arginine deiminase, type III QTL/Congenic 4 140,341,280 1.37 0.83 0.19 0.2 Epha2 Eph receptor A2 QTL/Congenic 4 140,857,155 0.41 0.41 28.41 20.82 Gm13154 predicted gene 13154 QTL/Congenic 4 146,927,386 0.95 1.31 5.08 3.52 2610305D13Rik RIKEN cDNA 2610305D13 gene QTL/Congenic 4 146,986,046 0.14 0.12 7.74 5.88 Clcn6 chloride channel 6 QTL/Congenic 4 147,378,368 3.46 3.48 11.99 9.88 2610109H07Rik RIKEN cDNA 2610109H07 gene QTL/Congenic 4 147,472,546 0.06 0.08 1.32 0.77 Ctnnbip1 catenin beta interacting protein 1 QTL/Congenic 4 148,892,345 0.38 0.25 1.28 1.45 Clstn1 calsyntenin 1 QTL/Congenic 4 148,960,577 0.31 0.53 2.85 2.12 Eno1 enolase 1, alpha non-neuron QTL/Congenic 4 149,610,830 25.54 15.78 67.77 69.2 Tnfrsf9 tumor necrosis factor receptor superfamily, member 9 QTL/Congenic 4 150,288,671 0.66 0.61 4.77 4.12 2010015L04Rik RIKEN cDNA 2010015L04 gene Congenic? 4 154,783,299 0.75 0.51 0.08 0.02 Agrn agrin 4 155,539,399 3.77 3.15 13.26 10.65 1700109H08Rik RIKEN cDNA 1700109H08 gene 5 3,571,566 2.07 4.15 1.21 0.7 Abcb1b ATP-binding cassette, sub-family B (MDR/TAP), member 1B 5 8,798,186 0.44 0.51 0.12 0.17 Abcb4 ATP-binding cassette, sub-family B (MDR/TAP), member 4 5 8,893,717 0.57 0.6 2.26 2.55 Fndc4 fibronectin type III domain containing 4 5 31,594,628 0.04 0.1 0.3 0.95 Nat8l N-acetyltransferase 8-like 5 34,338,633 0.31 0.23 0.88 0.97 Sorcs2 sortilin-related VPS10 domain containing receptor 2 5 36,359,829 0.69 0.52 0.08 0.12 Wfs1 Wolfram syndrome 1 homolog (human) 5 37,357,343 0.56 0.53 2.81 2.08 Pcdh7 protocadherin 7 5 58,109,339 0.61 0.39 0.1 0.25 Gm8397 predicted gene 8397 5 68,379,725 5.40 11.61 0.72 0.37 Cnga1 cyclic nucleotide gated channel alpha 1 5 72,994,935 0.57 1.25 4.53 3.61 Txk TXK tyrosine kinase 5 73,087,221 1.15 1.23 7.83 6.66 Ptpn13 protein tyrosine phosphatase, non-receptor type 13 5 103,854,211 0.89 1.44 4.24 6.54 Hfm1 HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae) 5 107,269,211 0.45 0.86 0.1 0.04 Cmklr1 chemokine-like receptor 1 5 114,062,363 0.44 0.45 1.78 1.49 Ift81 intraflagellar transport 81 homolog (Chlamydomonas) 5 123,000,213 0.42 0.75 1.94 2.96 Glt1d1 glycosyltransferase 1 domain containing 1 5 128,112,632 0.35 0.82 3.45 2.76 Gpr133 G protein-coupled receptor 133 5 129,602,625 2.75 2.65 0.23 0.23 Rasa4 RAS p21 protein activator 4 5 136,559,786 3.42 3.16 50.47 41.26 Ephb4 Eph receptor B4 5 137,791,337 0.25 0.08 1.88 2.12 Pdgfa platelet derived growth factor, alpha 5 139,451,968 10.97 3.74 27.92 25.12 Rpl21 ribosomal protein L21 5 147,644,466 16.54 20.79 0.69 0.72 Gm8615 predicted pseudogene 8615 5 149,967,022 0.92 0.89 7.7 7.56 Rpl30-ps1 ribosomal protein L3 6 38,326,807 5.35 11.42 27.23 26.69 Atp6v0e2 ATPase, H+ transporting, lysosomal V0 subunit E2 6 48,487,614 0.00 0 4.67 2.07

Page 3 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 Gimap7 GTPase, IMAP family member 7 6 48,668,620 0.98 1.75 0.36 0.46 Gimap3 GTPase, IMAP family member 3 6 48,715,088 0.19 0.27 1.05 1.2 Thnsl2 threonine synthase-like 2 (bacterial) 6 71,078,160 1.80 1.27 0.28 0.38 Reep1 receptor accessory protein 1 6 71,657,555 0.19 0.27 1.08 1.5 St3gal5 ST3 beta-galactoside alpha-2,3-sialyltransferase 2 6 72,047,607 0.47 0.29 1.1 1.2 Capg capping protein (actin filament), gelsolin-like 6 72,494,385 14.08 12.08 0.22 0.15 H1fx H1 histone family, member X 6 87,930,415 5.87 0.93 15.11 9.07 Plxna1 plexin A1 6 89,268,851 1.09 0.7 3.81 2.87 Suclg2 succinate-Coenzyme A ligase, GDP-forming, beta subunit 6 95,424,140 14.35 14.25 4.34 4.66 Camk1 calcium/calmodulin-dependent protein kinase I 6 113,284,118 1.22 0.79 7.24 7.8 Erc1 ELKS/RAB6-interacting/CAST family member 1 6 119,520,822 0.43 0.49 2.72 2.25 Leprel2 leprecan-like 2 6 124,791,107 0.33 0.31 1.35 0.85 C530028O21Rik RIKEN cDNA C530028O21 gene 6 124,946,712 0.42 0.55 2.53 2.66 Ltbr lymphotoxin B receptor 6 125,256,589 1.80 1.27 6.91 6.62 Clec12a C-type lectin domain family 12, member a 6 129,292,709 2.31 3.95 0.88 0.97 Bcl2l14 BCL2-like 14 (apoptosis facilitator) 6 134,346,336 11.19 9.79 2.77 2.47 Hebp1 heme binding protein 1 6 135,087,537 1.31 1.11 5.3 4.11 Art4 ADP-ribosyltransferase 4 6 136,796,972 10.02 11.63 0.73 0.26 Bcat1 branched chain aminotransferase 1, cytosolic 6 144,942,355 0.41 0.46 1.88 2.61 Rassf8 Ras association (RalGDS/AF-6) domain family (N-terminal) member 8 6 145,695,268 0.53 0.19 1.84 1.58 Bicd1 bicaudal D homolog 1 (Drosophila) 6 149,357,506 0.15 0.57 0.93 0.87 Gapdh glyceraldehyde-3-phosphate dehydrogenase 6 125111871 20.83 11.38 1.69 1.38 Eps8l1 EPS8-like 1 7 4,412,276 6.94 6.35 0.03 0 Zfp575 zinc finger protein 575 7 25,368,857 0.13 0.14 3.32 2.24 Megf8 myocyte enhancer factor 2C 7 26,102,183 2.46 1.87 8.69 7.49 Ceacam1 carcinoembryonic antigen-related cell adhesion molecule 1 7 26,246,721 0.36 0.32 0.05 0.08 Tmem91 transmembrane protein 91 7 26,454,158 2.28 2.54 32.15 18.73 Numbl numb-like 7 28,043,452 1.65 1.15 0.21 0.38 Zfp30 zinc finger protein 30 7 30,569,017 0.50 0.38 2.53 2.05 Mybpc2 myosin binding protein C, fast-type 7 51,757,088 0.48 0.21 1.4 0.74 Napsa napsin A aspartic peptidase 7 51,827,802 1.72 1.09 9.87 13.54 Kcnc3 potassium voltage gated channel, Shaw-related subfamily, member 3 7 51,846,034 0.02 0.01 0.47 0.27 Rgma RGM domain family, member A 7 80,520,406 0.02 0 0.33 0.81 Slco3a1 solute carrier organic anion transporter family, member 3a1 7 81,420,305 0.50 0.44 2.23 2.06 Acan aggrecan 7 86,198,369 0.16 0.27 2.19 2.55 Hddc3 HD domain containing 3 7 87,488,023 3.22 3.72 12.4 12.17 Gm5899 predicted pseudogene 5899 7 101,345,720 0.36 0.19 5.98 7.74 Myo7a myosin VIIA 7 105,199,570 0.76 0.42 0.13 0.22 Inppl1 inositol polyphosphate phosphatase-like 1 7 108,971,175 0.04 0.05 4.75 4.51 Trim12a tripartite motif-containing 12A 7 111,448,408 18.22 28.51 0.57 0.54 Trim30c tripartite motif-containing 30C 7 111,530,579 2.23 3.02 0.33 0.61 Gm5900 predicted pseudogene 5900 7 112,098,429 1.71 1.85 7.01 5.59 Trim3 tripartite motif-containing 3 7 112,752,977 0.40 0.43 1.08 1.49 Sbf2 SET binding factor 2 7 117,451,527 0.19 0.22 0.4 1.07

Page 4 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 Fosb FBJ osteosarcoma oncogene B 7 125,111,871 0.57 0.35 0.04 0.12 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta- Hsd3b7 isomerase 7 7 134,929,122 1.24 1.26 4 5.63 Gm6916 predicted pseudogene 6916 7 135,483,931 2.26 4 10.34 12.14 Dock1 dedicator of cytokinesis 1 7 141,862,370 0.54 0.35 2 2.05 Igf2 insulin-like growth factor 2 7 149,836,673 4.17 2.23 1.52 0.55 Igf2as insulin-like growth factor 2, antisense 7 149,845,598 0.74 0.45 0.23 0.05 Dennd5a DENN/MADD domain containing 5A 7 117037294 1.20 1.24 4.56 5.52 Gm7116 predicted gene 7116 8 4,582,892 0.01 0.01 0.52 0.43 Atp11a ATPase, class VI, type 11A 8 12,757,014 0.76 0.63 2.26 2.51 5830468F06Rik RIKEN cDNA 5830468F06 gene 8 15,015,092 19.79 22.13 5.87 4.74 Kbtbd11 kelch repeat and BTB (POZ) domain containing 11 8 15,024,319 4.02 3.99 0.85 0.7 Kbtbd11 kelch repeat and BTB (POZ) domain containing 11 8 15,024,319 18.72 18.12 3.68 3.91 Fgfr1 fibroblast growth factor receptor 1 8 26,624,126 1.28 0.84 3.68 4.77 Gsr glutathione reductase 8 34,762,995 31.86 33.93 6.29 5.63 Rbpms RNA binding protein gene with multiple splicing 8 34,893,116 1.32 1.02 0.29 0.5 Mfhas1 malignant fibrous histiocytoma amplified sequence 1 8 36,650,852 0.50 0.43 2.22 2.3 Tpd52-ps tumor protein D52, pseudogene 8 82,202,735 1.26 1.28 0.49 0.25 Cd97 CD97 antigen 8 86,247,150 1.16 0.86 7.11 13.83 Lphn1 latrophilin 1 8 86,424,004 3.70 1.7 9.38 8.71 Podnl1 podocan-like 1 8 86,649,888 2.00 3.25 13.03 12.29 Nanos3 nanos homolog 3 (Drosophila) 8 86,697,632 1.58 0.9 5.47 5.35 Ldhd lactate dehydrogenase D 8 114,150,171 1.58 1.44 5.95 4.45 Spire2 spire homolog 2 (Drosophila) 8 125,856,613 0.24 0.2 1.04 1.12 Fam89a family with sequence similarity 89, member A 8 127,264,157 1.83 3.15 0.22 0.5 Mef2b myocyte enhancer factor 2B 8 72676677 0.64 0.23 2.48 1.12 Gm5611 predicted gene 5611 9 16,834,489 5.41 7.83 17.38 22.18 Hspa8 heat shock protein 8 9 40,609,067 593.76 570.08 137.24 122.65 Ubash3b ubiquitin associated and SH3 domain containing, B 9 40,819,181 0.65 0.53 2.11 3.31 Sorl1 sortilin-related VPS10 domain containing receptor 2 9 41,772,803 0.87 0.59 3.83 3.1 Arhgef12 Rho guanine nucleotide exchange factor (GEF) 12 9 42,771,925 0.16 0.22 0.69 0.63 Fam55a family with sequence similarity 55, member A 9 48,224,381 0.21 0.14 1.82 3.32 Zbtb16 zinc finger and BTB domain containing 16 9 48,462,416 0.02 0.06 0.27 0.79 Coro2b coronin, actin binding protein, 2B 9 62,267,299 3.59 1.2 0.53 0.56 Tln2 talin 2 9 67,065,943 0.09 0.04 0.4 0.4 Myo1e myosin IE 9 70,055,157 0.04 0.11 0.31 0.45 Gcom1 GRINL1A complex locus 9 71,352,154 15.65 15.18 0.05 0.09 Rab27a RAB27A, member RAS oncogene family 9 72,892,672 42.20 42.31 5.01 5.9 C920006O11Rik RIKEN cDNA C920006O11 gene 9 78,023,721 1.50 1.71 0.55 0.29 Fam46a family with sequence similarity 46, member A 9 85,214,046 0.03 0.02 0.49 0.31 Rab6b RAB6B, member RAS oncogene family 9 103,014,404 7.59 9.46 0.75 0.3 Trf transferrin 9 103,111,206 3.60 2.65 8.87 10.82 Rpl29 ribosomal protein L29 9 106,331,785 33.20 19.54 0.24 0.35 Abhd14b abhydrolase domain containing 14b 9 106,350,992 3.40 3.18 0.56 0.57

Page 5 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 Hemk1 HemK methyltransferase family member 1 9 107,230,023 1.58 1.83 6.54 5.21 Lamb2 laminin, beta 2 9 108,382,277 0.82 0.21 3.41 2.32 Plxnb1 plexin B1 9 108,997,950 0.17 0.12 0.46 0.65 Ulk4 unc-51-like kinase 4 (C. elegans) 9 120,869,386 0.08 0.11 0.43 0.56 Ccr2 chemokine (C-C motif) receptor 2 9 124,016,689 0.29 1.27 0.25 0.11 Akap12 A kinase (PRKA) anchor protein (gravin) 12 10 5,987,070 1.26 0.94 3.85 5.21 Plagl1 pleiomorphic adenoma gene-like 1 10 12,810,497 0.06 0.02 0.61 1.26 H60b histocompatibility 60b 10 21,993,152 0.04 0.09 3.22 3.2 Ptprk protein tyrosine phosphatase, receptor type, K 10 27,794,626 0.41 0.32 1.71 0.99 Hal histidine ammonia lyase 10 92,951,513 0.30 0.51 4.23 2.82 Lrp1 low density lipoprotein receptor-related protein 1 10 126,975,217 7.54 4.76 34.14 26.65 Osbp2 oxysterol binding protein 2 11 3,603,734 0.15 0.09 0.4 0.97 Camk2b calcium/calmodulin-dependent protein kinase II, beta 11 5,869,647 0.73 0.28 0.04 0.01 Adcy1 adenylate cyclase 1 11 6,963,492 0.07 0.03 0.28 0.49 1110067D22Rik RIKEN cDNA 1110067D22 gene 11 20,723,579 0.12 0.09 0.77 0.6 Ccdc88a coiled coil domain containing 88A 11 29,273,658 0.78 1.93 4.03 3.77 Stc2 stanniocalcin 2 11 31,257,307 0.00 0 1.07 2.83 Butr1 butyrophilin related 1 QTL 11 58,731,410 0.09 0 3.77 2.59 Hist3h2ba histone cluster 3, H2ba QTL 11 58,762,422 4.90 3.63 0.84 0.47 B9d1 B9 protein domain 1 QTL 11 61,318,646 1.58 1.74 5.54 5.82 Fam83g family with sequence similarity 83, member G QTL 11 61,497,593 0.55 0.25 0.07 0.1 Trim16 tripartite motif-containing 16 QTL 11 62,633,733 2.21 2.33 16.85 20.32 Fbxw10 F-box and WD-40 domain protein 10 QTL 11 62,660,571 0.59 0.63 7.5 6.93 Myh10 myosin, heavy polypeptide 10, non-muscle QTL 11 68,505,061 2.33 1.73 8.2 11.75 Nlrp1b NLR family, pyrin domain containing 1A QTL 11 70,966,604 0.41 0.49 0.05 0.07 Tmem98 transmembrane protein 98 11 80,623,677 0.03 0 5.36 5.82 A930013B10Rik RIKEN cDNA A930013B10 gene 11 88,927,402 74.35 65.96 7.39 3.55 Gm525 predicted gene 525 11 88,935,155 19.08 16.69 2.29 0.79 Tom1l1 target of myb1-like 1 (chicken) 11 90,504,779 0.44 0.47 2.24 2.32 Rsad1 radical S-adenosyl methionine domain containing 1 11 94,401,112 1.53 1.43 0.44 0.49 Samd14 sterile alpha motif domain containing 14 11 94,871,193 0.67 0.72 2.19 2.86 E130012A19Rik RIKEN cDNA E130012A19 gene 11 97,488,703 0.87 0.32 1.47 2.24 Pcgf2 polycomb group ring finger 2 11 97,551,106 0.72 0.26 2.17 1.47 Tubg2 tubulin, gamma 2 11 101,017,221 0.45 0.21 2.03 2.27 Adam11 a disintegrin and metallopeptidase domain 11 11 102,622,753 1.89 0.92 15.17 12.05 Tanc2 tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1 11 105,451,300 0.32 0.4 1.2 1.12 2610035D17Rik RIKEN cDNA 2610035D17 gene 11 112,905,209 10.02 10.25 0 0 Cdr2l cerebellar degeneration-related protein 2-like 11 115,243,230 0.21 0.21 0.61 0.8 2210020M01Rik RIKEN cDNA 2210020M01 gene 11 115,761,280 14.54 18.61 3.44 5.91 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N- St6galnac2 acetylgalactosaminide alpha-2,6-sialyltransferase 1 11 116,536,617 0.20 0.39 4.76 6.72 BC018473 cDNA sequence BC018473 11 116,613,481 0.02 0 6.27 14.26 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N- St6galnac1 acetylgalactosaminide alpha-2,6-sialyltransferase 1 11 116,626,339 0.00 0 1.04 1.42

Page 6 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 Greb1 gene regulated by estrogen in breast cancer protein 12 16,677,421 0.06 0.08 4.98 4.09 Odc1 ornithine decarboxylase, structural 1 12 17,551,679 14.76 11.08 43.59 45.24 Gm9237 predicted pseudogene 9237 12 18,676,650 0.01 0.03 0.12 0.15 Gm9282 predicted gene 9282 12 22,010,172 0.00 0.01 0.29 0.42 Gm6969 predicted pseudogene 6969 12 25,323,534 4.02 4.35 22.94 20.98 Cmpk2 cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial 12 27,154,080 2.39 1.8 0.45 0.54 Hdac9 histone deacetylase 9 12 35,056,362 0.49 0.67 0 0.01 Prps1l1 phosphoribosyl pyrophosphate synthetase 1-like 1 12 35,669,445 0.66 1.46 0 0 Lrrn3 leucine rich repeat protein 3, neuronal 12 42,178,260 0.77 1.73 7.55 8.15 Akap6 A kinase (PRKA) anchor protein 6 12 53,800,370 1.08 0.98 0.07 0.28 Lrrc9 leucine rich repeat containing 9 12 73,542,853 0.00 0.03 0.4 0.68 Syne2 synaptic nuclear envelope 2 12 76,919,121 1.07 1.02 9.2 7.18 Esr2 estrogen receptor 2 (beta) 12 77,221,406 0.31 0.59 16.08 12.42 Rps6kl1 ribosomal protein S6 kinase-like 1 12 86,476,580 11.27 8.96 95.16 60.15 Pgf placental growth factor 12 86,507,591 0.65 0.54 2.36 1.69 Fos FBJ osteosarcoma oncogene 12 86,814,840 2.78 0.76 0.67 0.24 Rpl30-ps8 ribosomal protein L30, pseudogene 8 12 100,285,369 2.15 2.98 9.72 10.06 Evl Ena-vasodilator stimulated phosphoprotein 12 109,792,930 3.02 2.37 12.24 18.22 1200009I06Rik RIKEN cDNA 1200009I06 gene 12 112,655,800 0.23 0.2 0.84 0.9 Gm266 predicted gene 266 12 112,722,822 1.09 0.56 5.18 19.79 Akr1e1 aldo-keto reductase family 1, member E1 13 4,590,003 6.42 8.9 0.78 1.22 Ryr2 ryanodine receptor 2, cardiac QTL 13 11,645,370 0.02 0.01 5.55 4.02 Gm4933 predicted gene 4933 QTL 13 12,767,882 0.89 0.18 2.23 3.76 Epdr1 ependymin related protein 1 (zebrafish) QTL 13 19,683,575 0.31 0.06 1.4 1.42 Gm11346 predicted gene 11346 QTL 13 24,689,482 3.09 7.58 0.72 0.39 Aldh5a1 aldhehyde dehydrogenase family 5, subfamily A1 QTL 13 24,999,448 0.21 0.08 1.06 1.95 Dapk1 death associated protein kinase 1 QTL 13 60,703,308 12.06 11.33 2.13 0.89 Gm6436 predicted gene 6436 QTL 13 61,811,897 4.80 7.84 1.15 2.19 Habp4 hyaluronic acid binding protein 4 QTL 13 64,263,228 0.86 0.69 2.38 2.78 Gpx8 glutathione peroxidase 8 (putative) 13 113,832,971 0.64 0.42 2.34 1.8 Esm1 endothelial cell-specific molecule 1 13 113,999,867 5.07 5.91 1.05 1.97 Gm6404 predicted gene 6404 13 116,943,973 6.94 12.96 63.88 70.15 Emb embigin 13 118,009,432 15.30 15.53 2.22 2.77 Fbp1 fructose bisphosphatase 1 13 62966113 10.60 7.52 47.84 48.65 Acox2 acyl-Coenzyme A oxidase 2, branched chain 14 9,058,025 0.43 0.08 1.23 1.81 Zfp503 zinc finger protein 503 14 22,803,184 0.02 0.03 0.33 0.43 Rps24 ribosomal protein S24 14 25,309,903 495.64 657.37 82.87 87.26 Peli2 pellino 2 14 48,740,544 1.06 0.95 4.75 4.08 Ccnb1ip1 cyclin B1 interacting protein 1 14 51,408,924 0.00 0 2.3 1.6 Ndrg2 N-myc downstream regulated gene 2 14 52,524,956 2.64 2.15 0.46 0.5 Olfr1507 olfactory receptor 1507 14 53,109,696 1.81 4.1 0.06 0 Ppp1r3e protein phosphatase 1, regulatory (inhibitor) subunit 3E 14 55,491,518 0.98 0.93 0.26 0.18 Slc22a17 solute carrier family 22 (organic anion/cation transporter), member 15 14 55,525,578 1.23 1.94 6.95 4.59 Rec8 REC8 homolog (yeast) 14 56,236,874 1.47 3.1 0.43 0.39

Page 7 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 Atp8a2 ATPase, aminophospholipid transporter-like, class I, type 8A, member 2 14 60,266,368 0.50 0.37 1.65 4.86 Ptk2b PTK2 protein tyrosine kinase 2 14 66,772,094 9.56 7.74 42.09 36.6 Loxl2 lysyl oxidase-like 2 14 70,009,283 0.83 1.25 0 0 Cysltr2 cysteinyl leukotriene receptor 2 14 73,428,935 2.55 5.14 0.59 1.37 Tsc22d1 TSC22 domain family, member 1 14 76,814,768 20.43 21.57 7.54 5.72 Lmo7 LIM domain only 7 14 102,129,174 0.15 0.16 0.97 0.86 Tpm3-rs7 tropomyosin 3, related sequence 7 14 113,713,857 27.43 19.38 106.49 127.03 Gm7125 predicted pseudogene 7125 15 68,707,220 0.77 0.78 3.41 3.46 Ptk2 PTK2 protein tyrosine kinase 2 15 73,035,536 0.09 0.06 0.33 0.78 Ly6a lymphocyte antigen 6 complex, locus A 15 74,825,308 20.35 28.93 2.17 3.31 Ly6c1 lymphocyte antigen 6 complex, locus C1 15 74,875,447 12.96 14.6 0.14 0.15 C1qtnf6 C1q and tumor necrosis factor related protein 6 15 78,353,776 0.04 0.1 0.4 0.83 Card10 caspase recruitment domain family, member 10 15 78,605,568 5.92 2.53 0.27 0.09 Apobec3 apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3 15 79,722,888 64.43 66.51 19.17 16.81 Rpl3 ribosomal protein L3 15 79,908,225 504.17 425.07 99.46 111.25 Plxnb2 plexin B2 15 88,985,979 0.17 0.13 0.59 0.65 Lima1 LIM domain and actin binding 1 15 99,608,901 0.20 0.2 0.83 0.61 Gm5481 predicted gene 5481 16 16,275,696 0.50 1.13 3.31 4.56 solute carrier family 7 (cationic amino acid transporter, y+ system), Slc7a4 member 4 16 17,572,111 0.57 0.45 2.12 1.63 Rpl35a ribosomal protein L35A 16 33,056,539 285.94 324.62 19.67 26.69 Mylk myosin, light polypeptide kinase 16 34,745,296 0.12 0.08 0.26 0.36 Slc15a2 solute carrier family 15 (H+/peptide transporter), member 2 16 36,750,264 4.55 16.3 0 0 BC002163 cDNA sequence BC002163 16 42,955,744 12.27 10.44 52.32 45.41 Gm4827 predicted gene 4827 16 50,019,769 1.75 3.78 0.88 0.81 Gpr128 G protein-coupled receptor 128 16 56,724,722 0.10 0.28 1.08 1.22 1700024P12Rik RIKEN cDNA 1700024P12 gene 17 3,083,924 3.04 4.02 0.32 0.58 Ttll2 tubulin tyrosine ligase-like family, member 11 17 7,555,253 0.00 0.03 20.87 14.38 5830477G23Rik RIKEN cDNA 5830477G23 gene 17 7,603,874 0.36 0.54 10.75 8.07 Prr18 proline rich region 18 17 8,533,271 0.26 0.37 1.21 0.78 Pde10a phosphodiesterase 10A 17 8,718,237 0.21 0.08 0.35 0.78 Unc93a unc-93 homolog A (C. elegans) QTL 17 13,301,483 0.02 0 5.52 3.33 Tcte2 t-complex-associated testis expressed 2 QTL 17 13,675,419 0.06 0.33 7.82 4.63 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Mllt4 Drosophila); translocated to, 4 QTL 17 13,897,546 5.90 6.9 82.41 69.57 Prdm9 PR domain containing 9 QTL 17 15,682,083 1.75 1.08 4.02 4.86 Eif3s6-ps3 eukaryotic translation initiation factor 3, subunit 6, pseudogene 3 QTL 17 15,982,239 0.21 0.28 1.6 1.86 Prss30 protease, serine, 30 QTL 17 24,109,093 2.98 3.14 0.48 0.17 Tmprss3 transmembrane protease, serine 3 QTL 17 31,316,217 0.65 0.9 0.21 0.26 Rsph1 radial spoke head 1 homolog (Chlamydomonas) QTL 17 31,391,964 0.44 0.41 4.73 9.21 Gm8437 predicted gene 8437 QTL 17 31,430,697 1.76 1.61 4.43 6.13 Slc37a1 solute carrier family 37 (glycerol-3-phosphate transporter), member 2 QTL 17 31,432,428 7.19 5.68 18.81 26.48 Hsf2bp heat shock transcription factor 2 binding protein QTL 17 32,081,714 1.48 2.3 0 0 Zfp811 zinc finger protein 811 QTL 17 32,934,351 0.15 0.24 0.97 1.24

Page 8 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 Zfp870 zinc finger protein 870 QTL 17 33,019,616 0.08 0.14 0.39 0.51 Rps28 ribosomal protein S28 QTL 17 33,959,995 196.72 156.18 62.86 37.93 Rps18 ribosomal protein S18 QTL 17 34,088,944 949.30 795.05 73.23 70.56 H2-K2 histocompatibility 2, K region locus 2 QTL 17 34,112,431 1.30 1.58 7.54 6.8 AA388235 expressed sequence AA388235 QTL 17 34,118,437 1.06 1.12 0.15 0.12 H2-K1 histocompatibility 2, K1, K region QTL 17 34,132,958 252.76 236.48 56.13 57.89 H2-Pa histocompatibility 2, P region alpha locus QTL 17 34,221,558 0.38 0.61 2.62 2.34 H2-Oa histocompatibility 2, O region alpha locus QTL 17 34,229,377 3.01 2.41 10.41 9.18 H2-Ab1 histocompatibility 2, class II antigen A, beta 1 QTL 17 34400154 4.06 2.41 0.99 0.25 Notch4 NLR family, pyrin domain containing 1B QTL 17 34,701,213 0.24 0.37 2.11 2.61 Stk19-ps1 serine/threonine kinase 19, pseudogene 1 QTL 17 34,882,743 0.62 0.93 2.26 2.62 C4a complement component 4A (Rodgers blood group) QTL 17 34,946,037 0.06 0.09 0.64 0.73 Neu1 neuraminidase 1 QTL 17 35,068,324 10.25 9.16 36 30.85 H2-Q1 histocompatibility 2, Q region locus 1 QTL 17 35,457,507 0.30 0.23 2.27 2.39 H2-Q2 histocompatibility 2, Q region locus 2 QTL 17 35,479,278 0.33 0.68 7.01 9.3 H2-Q7 histocompatibility 2, Q region locus 7 QTL 17 35,576,161 29.02 60.19 9.13 12.44 H2-Q10 histocompatibility 2, Q region locus 10 QTL 17 35,607,034 0.37 0.61 4.05 3.8 2300002M23Rik RIKEN cDNA 2300002M23 gene QTL 17 35,704,430 2.29 1.59 157.49 105.6 Dpcr1 diffuse panbronchiolitis critical region 1 (human) QTL 17 35,772,700 0.00 0 1.27 0.87 Ddr1 discoidin domain receptor family, member 1 QTL 17 35,818,512 0.17 0.06 3.73 2.9 H2-Bl histocompatibility 2, blastocyst QTL 17 36,216,993 0.12 0.22 36.12 40.51 Gm8815 predicted gene 8815 QTL 17 36,245,531 0.12 0.13 0.6 0.56 C920025E04Rik RIKEN cDNA C920025E04 gene QTL 17 36,246,172 2.08 1.83 25.82 27.92 H2-T10 histocompatibility 2, T region locus 10 QTL 17 36,254,035 7.41 8.37 169.59 181.13 2410017I17Rik RIKEN cDNA 2410017I17 gene QTL 17 36,292,064 0.14 0.26 13.92 16.21 H2-T3 histocompatibility 2, T region locus 3 QTL 17 36,322,518 0.04 0.11 114.42 165.53 H2-M6-ps histocompatibility 2, M region locus 6, pseudogene QTL 17 37,106,140 0.00 0.13 3.18 5.12 Cyp39a1 cytochrome P450, family 39, subfamily a, polypeptide 1 QTL 17 43,804,374 0.09 0.11 0.16 0.82 Gm9104 predicted gene 9104 QTL 17 45,602,737 4.32 3.69 0.1 0.28 Vegfa vascular endothelial growth factor A QTL 17 46,153,942 6.27 6.16 32.82 28.8 Clip4 CAP-GLY domain containing linker protein family, member 4 17 72,131,287 0.13 0.08 0.99 0.6 Nlrc4 NLR family, CARD domain containing 4 17 74,825,635 0.05 0.1 0.24 0.83 Qpct glutaminyl-peptide cyclotransferase (glutaminyl cyclase) 17 79,451,246 0.87 1.03 0.09 0.18 Gm6594 predicted pseudogene 6594 17 82,938,598 0.97 1.1 3.87 4.02 Haao 3-hydroxyanthranilate 3,4-dioxygenase 17 84,230,696 2.49 1.42 0.23 0.3 Dync2li1 dynein cytoplasmic 2 light intermediate chain 1 17 85,025,836 0.52 0.53 1.61 1.99 Gm5503 predicted gene 5503 18 33,543,822 0.86 0.93 3.98 5.5 Epb4.1l4a erythrocyte protein band 4.1-like 4a 18 33,955,981 1.65 1.58 0.62 0.39 Egr1 early growth response 1 18 35,020,861 1.98 1.33 0.21 0.24 Gm6724 predicted gene 6724 18 35,129,314 3.09 3.3 17.2 19.77 Pcdhgc3 protocadherin gamma subfamily C, 3 18 37,966,064 0.39 0.38 1.36 1.56 Arhgap26 Rho GTPase activating protein 26 18 38,761,188 7.76 7.39 2.64 2.4 Prelid2 PRELI domain containing 2 18 42,035,350 5.30 8.33 24.81 26.86 4833403I15Rik RIKEN cDNA 4833403I15 gene 18 47,009,699 0.00 0 0.83 0.71

Page 9 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 Camk2a calcium/calmodulin-dependent protein kinase II alpha 18 61,085,272 15.73 16.09 0.95 1.04 Rpl21-ps8 ribosomal protein L21, pseudogene 8 18 82,692,936 11.65 26.46 0.61 0.5 Eif3s6-ps2 eukaryotic translation initiation factor 3, subunit 6, pseudogene 2 18 90,481,217 3.54 5.03 14.77 13.95 Bbs1 Bardet-Biedl syndrome 1 (human) 19 4,889,158 0.67 0.5 1.89 1.65 Tsga10ip testis specific 10 interacting protein 19 5,390,049 0.08 0.08 3.42 1.84 Ltbp3 latent transforming growth factor beta binding protein 3 19 5,740,904 0.13 0.09 0.52 0.34 Pcna-ps2 proliferating cell nuclear antigen pseudogene 2 19 9,357,869 7.51 9.71 53.99 64.23 Dtx4 deltex 4 homolog (Drosophila) 19 12,540,826 4.36 5.92 0.2 0.41 Gm5514 predicted gene 5514 19 22,012,569 2.61 2.03 10.89 8.78 Scd1 stearoyl-Coenzyme A desaturase 1 19 44,468,945 0.19 0.11 2.48 2.46 nuclear factor of kappa light polypeptide gene enhancer in B-cells 2, Nfkb2 p49/p100 19 46,380,108 36.42 23.68 7.44 5.75 Psd pleckstrin and Sec7 domain containing 19 46,386,577 5.97 4.38 1.1 0.9 Grk5 G protein-coupled receptor kinase 5 19 60,966,379 0.19 0.23 0.99 1.06 Porcn porcupine homolog (Drosophila) X 7,770,974 0.42 0.42 1.42 1.33 Lonrf3 LON peptidase N-terminal domain and ring finger 3 X 33,868,348 0.04 0.08 0.22 0.38 Rps24-ps3 ribosomal protein S24, pseudogene 3 X 76,440,386 43.87 59.2 1043 1270.8 Arhgef9 CDC42 guanine nucleotide exchange factor (GEF) 9 X 92,244,276 0.19 0.18 0.56 0.69 Tceal8 transcription elongation factor A (SII)-like 8 X 132,704,620 2.98 2.58 8.38 9.7 Bex1 brain expressed gene 1 X 132,748,511 0.21 0.16 3.88 8.78 Gm6472 predicted pseudogene 6472 X 149,344,009 12.99 17.36 172.86 198.28 Tlr7 toll-like receptor 7 X 163,742,861 0.24 0.79 1.15 1.72

1 QTL: Gene within a QTL peak region; Congenic: gene within the chr4 congenic region; Congenic?: Gene within the congenic crossover region. 2 Gene start site in base pairs based on mouse genome build NCBI3/mm9 3 Data are shown as Log2 transformed gene expression in RPKM (reads per Kb per million mapped reads) 4 Samples: B4: B6.Rag 4 wk; B7: B6.Rag 7 wk; N4: NOD.Rag 4 wk; N7: NOD.Rag 7 wk

Page 10 Supplemental Table 2. N7 genes expressed 3X higher than others

Alt name N4vB Gene MGI Description Diff1 chr Start Bp B4 B7 N4 N7 inverted formin, FH2 and WH2 domain 2610204M08Rik Inf2 containing 12 113,826,995 0.08 0.07 0.11 0.98 Amotl1 Amotl1 angiomotin-like 1 9 14,346,410 0.02 0.04 0.06 0.3 Bpil2 Bpil2 BPI fold containing family C 10 85,422,085 2.28 4.66 2.86 20.64 Cd2 Cd2 CD2 antigen yes 3 101,079,822 0.12 0 0.86 3.45 Cd244 Cd244 CD244 natural killer cell receptor 2B4 1 173,489,324 0.82 0.59 1.11 4.44 Cd5 Cd5 CD5 antigen 19 10,792,633 1.50 0.98 0.64 3.31 Cd7 Cd7 CD7 antigen 11 120,898,061 1.42 1.25 0.83 6.29 Cldn2 Cldn2 claudin 2 X 136,335,367 0.47 0.42 0.36 8.74 Clec4e Clec4e C-type lectin domain family 4, member e 6 123,231,807 0.15 0.28 0.21 3.43 Cygb Cygb cytoglobin yes 11 116,506,909 0.00 0 0.15 1.16 Dlk1 Dlk1 delta-like 1 homolog (Drosophila)yes 12 110,691,059 0.00 0.03 0.25 10.17 Dsp Dsp desmoplakin yes 13 38,243,197 0.06 0.08 0.21 1.07 E430002D04Rik Cd163l1 CD163 molecule-like 1 7 147,404,166 5.28 7.11 12.02 68.25 Emilin2 Emilin2 elastin microfibril interfacer 2 17 71,601,511 1.67 1.22 0.77 3.04 F2r F2r coagulation factor II (thrombin) receptor 13 96,371,744 3.02 3.13 3.36 18.66 Fbln1 Fbln1 fibulin 1 15 109,006,845 0.39 0.08 0.25 1.47 Fndc1 Fndc1 fibronectin type III domain containing 1 17 7,931,434 0.14 0.3 0.01 1.16 Gm266 Gm266 predicted gene 266 yes 12 112,722,822 1.09 0.56 5.18 19.79 Gm770 Ccdc135 coiled-coil domain containing 135 8 97,579,003 1.34 0.78 1.07 4.53 Gpr146 Gpr146 G protein-coupled receptor 146 5 139,853,696 0.18 0.23 0.16 0.86 Gpr97 Gpr97 G protein-coupled receptor 97 8 97,541,632 3.13 2.22 2.8 21.59 Gzmb Gzmb granzyme B 14 56,877,693 0.32 0.53 0.41 7.67 Hhex Hhex hematopoietically expressed homeobox 19 37,509,331 1.33 0.64 0.68 6.5 Htra3 Htra3 HtrA serine peptidase 3 yes 5 35,994,690 0.27 0.05 1.34 4.82 Itgb7 Itgb7 integrin beta 7 15 102,046,426 1.43 1.54 1.41 18.03 Itlna Itln1 intelectin 1 (galactofuranose binding) yes 1 173,448,253 0.00 0 0.15 1.53 Kifc3 Kifc3 kinesin family member C3 8 97,623,732 2.65 2.03 2.31 8.49 Kit Kit kit oncogene 5 75,970,941 6.00 4.25 6.33 19.37 Klf2 Klf2 Kruppel-like factor 2 (lung) 8 74,842,932 0.65 0.86 0.87 10.98 linker for activation of T cells family, member Lat2 Lat2 2 5 135,076,138 4.23 6.72 3.46 14.63 Lmcd1 Lmcd1 LIM and cysteine-rich domains 1 6 112,223,752 0.50 0.42 0.76 2.83 Lmo2 Lmo2 LIM domain only 2 2 103,798,143 0.24 0.11 0.44 5

1 Supplemental Table 2. N7 genes expressed 3X higher than others

Alt name N4vB Gene MGI Description Diff1 chr Start Bp B4 B7 N4 N7 Lrrc4b Lrrc4b leucine rich repeat containing 4B yes 7 51,684,388 0.02 0.14 0.51 3.87 Lyl1 Lyl1 lymphoblastomic leukemia 1 8 87,225,356 3.02 1.47 0.9 8.39 MAM domain containing Mdga1 Mdga1 glycosylphosphatidylinositol anchor 1 17 29964901 0.64 0.35 0.56 6.12 Mef2c Mef2c myocyte enhancer factor 2C 13 83,643,194 0.66 2.14 1.39 5.61 Mt1 Mt1 metallothionein 1 8 96,703,127 2.19 6.69 9.53 62.48 Mt2 Mt2 metallothionein 2 8 96,696,518 0.50 3.56 3.75 36.39 Odz4 Odz4 odd Oz/ten-m homolog 4 (Drosophila) 7 103,319,754 0.11 0.07 0.05 0.5 purinergic receptor P2X, ligand-gated ion P2rx7 P2rx7 channel, 7 5 123,093,920 0.13 0.12 0.13 0.59 S100a4 S100a4 S100 calcium binding protein A4 3 90,407,693 0.84 1.24 0.35 4.62 Samhd1 Samhd1 SAM domain and HD domain, 1 2 156,923,269 0.25 0.23 0.15 1.25 serine (or cysteine) peptidase inhibitor, clade Serpinh1 Serpinh1 H, member 1 yes 7 106,493,886 0.04 0.04 0.51 2.35 solute carrier family 7 (cationic amino acid Slc7a8 Slc7a8 transporter, y+ system), member 4 yes 14 55,341,053 0.06 0.08 0.75 8.18 Sprn Sprn shadow of prion protein 7 147,336,527 0.02 0.1 0.15 12.03 ST3 beta-galactoside alpha-2,3- St6gal1 St6gal1 sialyltransferase 5 16 23,224,813 0.10 0.13 0.03 0.39 Tas1r1 Tas1r1 taste receptor, type 1, member 1 4 151,402,023 0.34 0.3 0.5 1.89 Tes Tes testis derived transcript 6 17,015,149 2.62 2.79 1.57 6.03 Trib2 Trib2 tribbles homolog 2 (Drosophila) 12 15,798,533 0.79 1.01 0.66 3.24 Trim58 Trim58 tripartite motif-containing 58 11 58,453,967 0.00 0.15 0.13 1.67 Tspan32 Tspan32 tetraspanin 32 7 150,190,951 0.31 0.13 0.19 1.25 Zfp316 Zfp316 zinc finger protein 316 5 144,011,376 0.13 0.11 0.11 0.71

1 Genes that are also elevated in N4 in comparison with B6 (B4 and B7)

2