Regateiro et al Supplementary Figure 1 A 4 4 10 10 Marilyn Marilyn.Foxp3-/- 3 103 10 RII 2 β 2 10 10 TGF 1 101 10 1 2 3 4 3 4 10 10 10 10 101 102 10 10 CD4 B Supplementary Figure 1 A. Marilyn.Foxp3-/- CD4+ T cells express similar levels of TGFβRII to wildtype Marilyn CD4+ T cells. Splenic CD4+ T cells from Marilyn or Marilyn.Foxp3-/- were stained with anti-CD4-APC and anti-TGFβRII-PE. Red dots represent control isotype (PE) staining, blue dots represent staining for TGFβRII. B. Very few Marilyn CD4+ T cells are needed to reject a male skin graft in female B6.Rag-/- recepients. FACS analysis was performed to determine the proportion of CD4+ cells in female Marilyn spleens. Splenocytes were stained with both anti-CD4-FITC and anti-CD4-PE antibodies and an average of the two was deemed as the CD4+ percentage (2.4%). Whole splenocytes containing the required number of CD4+ cells were then transferred into female B6.Rag-/- recipients. Various numbers of CD4+ cells were transferred and the mice grafted with a male CBA.Rag-/- skin on the following day. Grafts were monitored on a daily basis. Difference in rejection kinetics between the groups was not statistically significant. Regateiro et al Supplementary Table I Probe log ratio Set ID T/UT p-value Gene Symbol mRNA - Description mRNA Accession 6782286 3.609099 3.03E-07 Itgae integrin alpha E, epithelial-associated NM_008399 (Itgae), transcript variant 1, mRNA. 6991192 3.391555 3.03E-07 Nt5e 5' nucleotidase, ecto (Nt5e), mRNA. NM_011851 6931759 3.345072 4.09E-05 Kit kit oncogene (Kit), transcript variant 1, NM_001122733 mRNA. 6759549 3.052253 2.12E-08 Ikzf2 IKAROS family zinc finger 2 (Ikzf2), mRNA. NM_011770 6861751 2.519725 8.91E-08 D18Ertd653e DNA segment, Chr 18, ERATO Doi 653, BC096371 expressed, mRNA (cDNA clone MGC:106263 IMAGE:3583946), complete cds. 6905818 2.43495 6.24E-08 Ift80 intraflagellar transport 80 homolog NM_026641 (Chlamydomonas) (Ift80), mRNA. 6910668 2.332868 2.77E-07 St6galnac3 // ST6 (alpha-N-acetyl-neuraminyl-2,3-beta- NM_011372 St6galnac3 galactosyl-1, 3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 (St6galnac3), mRNA. 7007950 2.192809 0.000363 Olfr46 olfactory receptor 46 (Olfr46), mRNA. NM_146934 6895856 2.096735 0.004338 Car2 carbonic anhydrase 2 (Car2), mRNA. NM_009801 6777309 2.058745 8.26E-05 Lyz2 lysozyme 2 (Lyz2), mRNA. NM_017372 6848579 1.994756 0.000346 Ccr6 chemokine (C-C motif) receptor 6 (Ccr6), NM_009835 transcript variant 1, mRNA. 6908461 1.890582 0.000161 S1pr1 sphingosine-1-phosphate receptor 1 NM_007901 (S1pr1), mRNA. 6792832 1.882423 2.91E-05 Cd7 CD7 antigen (Cd7), mRNA. NM_009854 6917997 1.803919 1.02E-06 Camk2n1 calcium/calmodulin-dependent protein NM_025451 kinase II inhibitor 1 (Camk2n1), mRNA. 6763731 1.796393 0.000556 Xcl1 chemokine (C motif) ligand 1 (Xcl1), NM_008510 mRNA. 6955698 1.772842 1.93E-05 Lrig1 leucine-rich repeats and immunoglobulin- NM_008377 like domains 1 (Lrig1), mRNA. 6748889 1.732433 4.29E-05 Il18r1 interleukin 18 receptor 1 (Il18r1), transcript NM_008365 variant 1, mRNA. 6837614 1.723663 1.96E-05 Cerk ceramide kinase (Cerk), mRNA. NM_145475 6764650 1.718202 1.66E-05 Ephx1 epoxide hydrolase 1, microsomal (Ephx1), NM_010145 mRNA. 6876914 1.664382 0.000138 Acvr2a activin receptor IIA (Acvr2a), mRNA. NM_007396 6757898 1.643344 7.89E-06 Neurl3 neuralized homolog 3 homolog NM_153408 (Drosophila) (Neurl3), mRNA. 6986359 1.614005 0.002372 Defa21 defensin, alpha, 21 (Defa21), mRNA. NM_183253 6802098 1.608321 3.6E-05 Actn1 actinin, alpha 1 (Actn1), mRNA. NM_134156 6791310 1.597657 1.54E-05 Ccr7 chemokine (C-C motif) receptor 7 (Ccr7), NM_007719 mRNA. 6873368 1.584057 4.75E-05 Kcnip2 Kv channel-interacting protein 2 (Kcnip2), NM_145703 transcript variant a, mRNA. 6840112 1.571175 1.39E-05 BC106179 cDNA sequence BC106179, mRNA (cDNA BC106179 clone MGC:118427 IMAGE:6509459), complete cds. 6919417 1.564054 2.78E-06 Tox thymocyte selection-associated high NM_145711 mobility group box (Tox), mRNA. 6946920 1.562271 0.006492 Cd8a CD8 antigen, alpha chain (Cd8a), NM_001081110 transcript variant 1, mRNA. 6884820 1.524667 0.002764 St8sia6 ST8 alpha-N-acetyl-neuraminide alpha-2,8- NM_145838 sialyltransferase 6 (St8sia6), mRNA. 6755216 1.514428 0.000115 Slamf6 SLAM family member 6 (Slamf6), mRNA. NM_030710 6954269 1.507733 0.000367 Hpgds hematopoietic prostaglandin D synthase NM_019455 (Hpgds), mRNA. 6963006 1.492523 0.000944 Pde2a phosphodiesterase 2A, cGMP-stimulated NM_001143848 (Pde2a), transcript variant 1, mRNA. 6791230 1.460221 0.001001 Arl5c ADP-ribosylation factor-like 5C (Arl5c), NM_207231 mRNA. 6764274 1.431221 0.000696 Ifi203 interferon activated gene 203 (Ifi203), NM_001045481 transcript variant 1, mRNA. 6788172 1.429802 2.1E-05 Tcf7 transcription factor 7, T-cell specific (Tcf7), NM_009331 mRNA. 6899683 1.380406 0.0002 Ctss cathepsin S (Ctss), mRNA. NM_021281 6769481 1.374489 0.000589 Btbd11 BTB (POZ) domain containing 11 (Btbd11), NM_028709 transcript variant 1, mRNA. 6898241 1.363875 6.62E-06 Smc4 structural maintenance of chromosomes 4 NM_133786 (Smc4), mRNA. 6886101 1.359014 0.001778 Olfr351 olfactory receptor 351 (Olfr351), mRNA. NM_146942 6844653 1.352185 0.000136 Bcl6 B-cell leukemia/lymphoma 6 (Bcl6), NM_009744 mRNA. 6848553 1.34033 0.001044 Tagap T-cell activation Rho GTPase-activating NM_145968 protein (Tagap), mRNA. 6888681 1.336101 0.007181 Olfr1270 olfactory receptor 1270 (Olfr1270), mRNA. NM_146985 6792649 1.310334 0.0001 Timp2 tissue inhibitor of metalloproteinase 2 NM_011594 (Timp2), mRNA. 6810260 1.307509 3.28E-05 Il6st interleukin 6 signal transducer (Il6st), NM_010560 mRNA. 6783489 1.30335 0.000129 Mmd monocyte to macrophage differentiation- NM_026178 associated (Mmd), mRNA. 6841019 1.301827 1.91E-05 Zbtb20 zinc finger and BTB domain containing 20 NM_019778 (Zbtb20), transcript variant 1, mRNA. 6850308 1.294014 0.00102 Olfr111 olfactory receptor 111 (Olfr111), mRNA. NM_001005485 6935408 1.281461 9.81E-05 Cyth3 cytohesin 3 (Cyth3), transcript variant 1, NM_011182 mRNA. 6768076 1.255537 9.29E-05 Smpdl3a sphingomyelin phosphodiesterase, acid- NM_020561 like 3A (Smpdl3a), mRNA. 6805430 1.25248 0.000121 Cmah cytidine monophospho-N-acetylneuraminic NM_001111110 acid hydroxylase (Cmah), transcript variant 2, mRNA. 6808964 1.234387 0.001289 Serinc5 serine incorporator 5 (Serinc5), mRNA. NM_172588 6790290 1.23392 0.000331 Ccl6 chemokine (C-C motif) ligand 6 (Ccl6), NM_009139 mRNA. 6820219 1.233595 0.000139 Lpar6 lysophosphatidic acid receptor 6 (Lpar6), NM_175116 mRNA. 7015465 1.230841 0.000855 Ssxb2 synovial sarcoma, X member B, breakpoint NM_001001450 2 (Ssxb2), transcript variant 1, mRNA. 6969994 1.229294 0.004665 Olfr68 olfactory receptor 68 (Olfr68), mRNA. NM_013620 7020802 1.212492 0.000176 Tlr7 toll-like receptor 7 (Tlr7), mRNA. NM_133211 6848721 1.203569 0.000183 --- cdna:known ENSMUST00000161890 chromosome:NCBIM37:17:13008797:1302 3201:1 gene:ENSMUSG00000078247 6980578 1.202565 0.002063 Rasa3 RAS p21 protein activator 3 (Rasa3), NM_009025 mRNA. 7015521 1.200518 0.005351 Cybb cytochrome b-245, beta polypeptide NM_007807 (Cybb), mRNA. 6955879 1.194786 2.17E-05 Foxp1 forkhead box P1 (Foxp1), transcript variant NM_053202 1, mRNA. 6822946 1.18296 0.000244 Nr1d2 nuclear receptor subfamily 1, group D, NM_011584 member 2 (Nr1d2), mRNA. 6778284 1.180345 0.002406 Pik3ip1 phosphoinositide-3-kinase interacting NM_178149 protein 1 (Pik3ip1), mRNA. 6923411 1.172697 0.007362 Jun Jun oncogene (Jun), mRNA. NM_010591 6790291 1.170038 5.13E-05 Ccl9 chemokine (C-C motif) ligand 9 (Ccl9), NM_011338 mRNA. 6833311 1.155539 0.000157 Nr4a1 nuclear receptor subfamily 4, group A, NM_010444 member 1 (Nr4a1), mRNA. 6848718 1.147284 0.000139 Airn antisense Igf2r RNA (Airn), transcript NR_027784 variant 4, antisense RNA. 6808876 1.135916 0.000361 Ssbp2 single-stranded DNA binding protein 2 NM_024272 (Ssbp2), transcript variant 2, mRNA. 6933441 1.133614 0.009838 --- cdna:known ENSMUST00000129007 chromosome:NCBIM37:5:110950181:1109 54999:1 gene:ENSMUSG00000048215 6969948 1.127802 0.008469 Olfr33 olfactory receptor 33 (Olfr33), mRNA. NM_147073 6902880 1.119946 0.001368 Wls wntless homolog (Drosophila) (Wls), NM_026582 mRNA. 6921012 1.112982 1.87E-06 Aqp3 aquaporin 3 (Aqp3), mRNA. NM_016689 6810548 1.110857 7.93E-05 Emb embigin (Emb), mRNA. NM_010330 6880776 1.099152 0.000189 Sema6d sema domain, transmembrane domain NM_199241 (TM), and cytoplasmic domain, (semaphorin) 6D (Sema6d), transcript variant 4, mRNA. 6942376 1.096305 0.009594 Ncf1 neutrophil cytosolic factor 1 (Ncf1), mRNA. NM_010876 6836954 1.094861 0.002967 Apol7b apolipoprotein L 7b (Apol7b), mRNA. NM_001024848 6786673 1.084076 0.000393 Rel reticuloendotheliosis oncogene (Rel), NM_009044 mRNA. 6892032 1.080852 0.00031 Acss1 acyl-CoA synthetase short-chain family NM_080575 member 1 (Acss1), nuclear gene encoding mitochondrial protein, mRNA. 6862133 1.07929 0.000181 Smad7 MAD homolog 7 (Drosophila) (Smad7), NM_001042660 mRNA. 6879998 1.056416 0.006895 Olfr1288 olfactory receptor 1288 (Olfr1288), mRNA. NM_146400 6803113 1.048371 0.000375 Gpr68 G protein-coupled receptor 68 (Gpr68), NM_175493 transcript variant 1, mRNA. 6758001 1.046924 0.000215 Aff3 AF4/FMR2 family, member 3 (Aff3), NM_010678 mRNA. 6870424 1.046841 0.000686 Add3 adducin 3 (gamma) (Add3), transcript NM_001164099 variant 1, mRNA. 6866257 1.041162 0.00229 Mc4r melanocortin 4 receptor (Mc4r), mRNA. NM_016977 6790531 1.040432 0.003029 Ypel2 yippee-like 2 (Drosophila) (Ypel2), mRNA. NM_001005341 6836325 1.036394 0.00089 Tmem71 transmembrane protein 71 (Tmem71), NM_172514 mRNA. 6878712 1.034908 0.00055 Slc43a1 solute carrier family 43, member 1 NM_001081349 (Slc43a1), transcript variant 1, mRNA. 6878045 1.029235 0.000399 --- cdna:known ENSMUST00000151236 chromosome:NCBIM37:2:71978785:72001 443:1 gene:ENSMUSG00000049044 6871509 1.02794 0.006802 Cd5 CD5 antigen (Cd5), mRNA. NM_007650 6986722 1.02683 0.001061 Mmp12 matrix metallopeptidase 12 (Mmp12), NM_008605 mRNA. 6949744 1.010036 0.000113 Clec4n C-type lectin domain family 4, member n NM_020001 (Clec4n), transcript variant 1, mRNA. 6930383 1.005898 0.002709 Cd38 CD38 antigen (Cd38), mRNA. NM_007646 6988958 1.005195 0.007024 Usp28 ubiquitin specific peptidase 28 (Usp28), NM_175482 mRNA.