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List of genes upregulated in Treg-DC compared to mat-DC Probeset ID Gene symbol Description adj.P.Val Fold-change (mat-DC: Treg-DC) ILMN_1676663 TNFRSF11B tumor necrosis factor receptor superfamily, member 11b 0.027025 0.126219 ILMN_1815023 PIM1 Pim-1 proto-oncogene, serine/threonine kinase 0.030375 0.169854 ILMN_1713397 NCCRP1 non-specific cytotoxic cell receptor protein 1 homolog (zebrafish) 0.049059 0.208023 ILMN_1744381 SERPINE1 serpin peptidase inhibitor, clade E (nexin, plasminogen activator 0.030375 0.218185 inhibitor type 1), member 1 ILMN_1747271 ATP1B2 ATPase, Na+/K+ transporting, beta 2 polypeptide 0.029882 0.228563 ILMN_1686109 CCL23 chemokine (C-C motif) ligand 23 0.033803 0.230626 ILMN_2327860 MAL mal, T-cell differentiation protein 0.043188 0.241969 ILMN_2390853 CTSH cathepsin H 0.022457 0.247506 ILMN_1738742 PLAT plasminogen activator, tissue 0.044522 0.262598 ILMN_2376205 LTB lymphotoxin beta (TNF superfamily, member 3) 0.043188 0.263951 ILMN_1800317 WNT5A wingless-type MMTV integration site family, member 5A 0.031472 0.267937 ILMN_1790881 HNMT histamine N-methyltransferase 0.027025 0.270653 ILMN_2192072 MMP7 matrix metallopeptidase 7 (matrilysin, uterine) 0.030375 0.272007 ILMN_1796094 CD36 CD36 molecule (thrombospondin receptor) 0.042418 0.278712 ILMN_1662451 FCER2 Fc fragment of IgE, low affinity II, receptor for (CD23) 0.030375 0.279015 solute carrier family 4, sodium bicarbonate cotransporter, member ILMN_2200917 SLC4A7 7 0.029882 0.281025 ILMN_2181241 RPL23AP64 ribosomal protein L23a pseudogene 64 0.030375 0.296740 ILMN_1712985 C17orf58 chromosome 17 open reading frame 58 0.031622 0.299285 ILMN_1685403 MMP7 matrix metallopeptidase 7 (matrilysin, uterine) 0.0393 0.305544 ILMN_1794803 NDP Norrie disease (pseudoglioma) 0.029882 0.306483 ILMN_1784630 KBTBD11 kelch repeat and BTB (POZ) domain containing 11 0.030375 0.316027 ILMN_2079386 RPL22 ribosomal protein L22 0.030375 0.327396 ILMN_1812191 C12orf57 chromosome 12 open reading frame 57 0.029882 0.333240 ILMN_1785646 PMP22 peripheral myelin protein 22 0.048102 0.334843 ILMN_1795304 CRLF2 cytokine receptor-like factor 2 0.043036 0.335395 ILMN_2318725 EEF1B2 eukaryotic translation elongation factor 1 beta 2 0.030375 0.335963 ILMN_1798256 UPP1 uridine phosphorylase 1 0.043799 0.339828 ILMN_2261416 CD3D CD3d molecule, delta (CD3-TCR complex) 0.043036 0.341891 ILMN_1700515 C17orf58 chromosome 17 open reading frame 58 0.043188 0.342892 ILMN_3241051 RPL32P18 ribosomal protein L32 pseudogene 18 0.036577 0.358019 Supplementary Table 1 (contd). List of genes upregulated in Treg-DC compared to mat-DC Probeset ID Gene symbol Description adj.P.Val Fold-change (mat-DC: Treg-DC) ILMN_1756541 MXD4 MAX dimerization protein 4 0.031277 0.358351 ILMN_1723035 OLR1 oxidized low density lipoprotein (lectin-like) receptor 1 0.030375 0.360042 ILMN_1699208 NAP1L1 nucleosome assembly protein 1-like 1 0.037541 0.361912 ILMN_2388975 CERK ceramide kinase 0.036577 0.368722 ILMN_1764030 CCL23 chemokine (C-C motif) ligand 23 0.036577 0.373796 ILMN_1663119 DSC2 desmocollin 2 0.037541 0.374818 ILMN_1671116 XXYLT1 xyloside xylosyltransferase 1 0.036577 0.392739 ILMN_1656537 SNRPN small nuclear ribonucleoprotein polypeptide N 0.043188 0.394753 ILMN_2083469 IRS2 insulin receptor substrate 2 0.037541 0.398079 ILMN_1719224 LRRC75A-AS1 LRRC75A antisense RNA 1 0.037541 0.403051 ILMN_1812321 FAM131C family with sequence similarity 131, member C 0.037541 0.411638 ILMN_2276904 ALOX15B arachidonate 15-lipoxygenase, type B 0.042858 0.419460 ILMN_2211065 TMEM91 transmembrane protein 91 0.043188 0.419538 ILMN_1795715 DPYD dihydropyrimidine dehydrogenase 0.04348 0.422688 ILMN_1729318 TOR1AIP1 torsin A interacting protein 1 0.042985 0.425158 ILMN_1906187 LOC283070 uncharacterized LOC283070 0.043188 0.425711 ILMN_1815292 RPL7 ribosomal protein L7 0.042826 0.429960 ILMN_1775708 SLC2A3 solute carrier family 2 (facilitated glucose transporter), member 3 0.042826 0.431491 ILMN_1761463 EFHD2 EF-hand domain family, member D2 0.042418 0.434978 ILMN_1763386 BID BH3 interacting domain death agonist 0.043188 0.450652 ILMN_2128967 C11orf1 chromosome 11 open reading frame 1 0.043188 0.453836 Supplementary Table 2. List of genes downregulated in Treg-DC compared to mat-DC Probeset ID Gene symbol Description adj.P.Val Fold-change (mat-DC: Treg-DC) ILMN_1791759 CXCL10 chemokine (C-X-C motif) ligand 10 0.029882 47.240283 ILMN_2067890 CXCL11 chemokine (C-X-C motif) ligand 11 0.020554 20.515951 ILMN_1739428 IFIT2 interferon-induced protein with tetratricopeptide repeats 2 0.037541 18.536452 ILMN_1701789 IFIT3 interferon-induced protein with tetratricopeptide repeats 3 0.031277 16.638422 ILMN_1801307 TNFSF10 tumor necrosis factor (ligand) superfamily, member 10 0.005969 14.780260 ILMN_1657871 RSAD2 radical S-adenosyl methionine domain containing 2 0.030375 11.475962 ILMN_2058782 IFI27 interferon, alpha-inducible protein 27 0.049059 10.575324 ILMN_1772964 CCL8 chemokine (C-C motif) ligand 8 0.027025 10.236912 ILMN_1813338 LAG3 lymphocyte-activation gene 3 0.005969 9.841286 ILMN_1745356 CXCL9 chemokine (C-X-C motif) ligand 9 0.019928 9.740089 ILMN_1674811 OASL 2'-5'-oligoadenylate synthetase-like 0.031277 9.390935 ILMN_1796409 C1QB complement component 1, q subcomponent, B chain 0.019928 8.306914 ILMN_1653466 HES4 hes family bHLH transcription factor 4 0.029882 7.420680 ILMN_1680339 PDGFRL platelet-derived growth factor receptor-like 0.037541 6.795421 ILMN_1665865 IGFBP4 insulin-like growth factor binding protein 4 0.020554 6.710888 ILMN_2233783 CD38 CD38 molecule 0.029882 6.051429 ILMN_1785902 C1QC complement component 1, q subcomponent, C chain 0.027025 6.030831 ILMN_3240420 USP18 ubiquitin specific peptidase 18 0.036692 5.843263 ILMN_1730229 CGNL1 cingulin-like 1 0.030375 5.746096 ILMN_1760062 IFI44 interferon-induced protein 44 0.045646 5.659766 ILMN_1670305 SERPING1 serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 0.030375 5.427818 ILMN_1792506 PLA1A phospholipase A1 member A 0.043036 5.276571 ILMN_2235851 NEURL3 neuralized E3 ubiquitin protein ligase 3 0.037455 5.074091 ILMN_1763523 HARS histidyl-tRNA synthetase 0.029882 4.999156 ILMN_1740466 FAM46A family with sequence similarity 46, member A 0.042826 4.744491 ILMN_1711702 CLEC2D C-type lectin domain family 2, member D 0.030375 4.678188 ILMN_1686664 MT2A metallothionein 2A 0.036577 4.640315 ILMN_1672024 ISCA1P1 iron-sulfur cluster assembly 1 pseudogene 1 0.049059 4.292038 ILMN_1700268 QPRT quinolinate phosphoribosyltransferase 0.030375 4.261784 ILMN_2038775 TUBB2A tubulin, beta 2A class IIa 0.030375 4.115890 ILMN_1752592 HLA-DRB4 major histocompatibility complex, class II, DR beta 4 0.036577 3.994790 ILMN_1769129 CCL19 chemokine (C-C motif) ligand 19 0.030375 3.989847 Supplementary Table 2 (contd). List of genes downregulated in Treg-DC compared to mat-DC Probeset ID Gene symbol Description adj.P.Val Fold-change (mat-DC: Treg-DC) ILMN_1710962 TMEM97 transmembrane protein 97 0.043188 3.910803 ILMN_1756374 SYCP1 synaptonemal complex protein 1 0.029882 3.894483 ILMN_1691156 MT1A metallothionein 1A 0.037455 3.894124 ILMN_1652065 KCNMB1 potassium large conductance calcium-activated channel, 0.029657 3.765643 subfamily M, beta member 1 ILMN_2053415 LDLR low density lipoprotein receptor 0.048102 3.740658 ILMN_1758323 ACPP acid phosphatase, prostate 0.030375 3.675483 ILMN_1808661 TOMM5 translocase of outer mitochondrial membrane 5 homolog 0.030375 3.574538 (yeast) ILMN_2287276 FAM177A1 family with sequence similarity 177, member A1 0.037455 3.505116 ILMN_1727271 WARS tryptophanyl-tRNA synthetase 0.043099 3.504966 ILMN_1790891 CKAP4 cytoskeleton-associated protein 4 0.038228 3.329990 ILMN_1769520 UBE2L6 ubiquitin-conjugating enzyme E2L 6 0.049059 3.317371 ILMN_1715931 ISCA1 iron-sulfur cluster assembly 1 0.043188 3.251217 ILMN_1720083 EHD4 EH-domain containing 4 0.029882 3.227800 ILMN_1680874 TUBB2B tubulin, beta 2B class IIb 0.036577 3.179411 ILMN_1753758 IL27 interleukin 27 0.042985 3.149064 ILMN_1698725 FRMD3 FERM domain containing 3 0.037455 3.072551 ILMN_1797728 HMGCS1 3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble) 0.030375 3.069864 ILMN_1663866 TGFBI transforming growth factor, beta-induced, 68kDa 0.037541 3.011580 ILMN_1660086 MYH11 myosin, heavy chain 11, smooth muscle 0.042985 2.987254 ILMN_2073604 EBP emopamil binding protein (sterol isomerase) 0.044845 2.981672 ILMN_1815626 DHCR7 7-dehydrocholesterol reductase 0.032789 2.946719 ILMN_1666594 IRF8 interferon regulatory factor 8 0.030375 2.880463 ILMN_1814726 SCARB2 scavenger receptor class B, member 2 0.031277 2.849468 ILMN_1677827 TLR7 toll-like receptor 7 0.037541 2.821970 ILMN_1789436 DENND1B DENN/MADD domain containing 1B 0.036577 2.802004 ILMN_3247560 BSPRY B-box and SPRY domain containing 0.030375 2.787414 ILMN_1674386 PITX1 paired-like homeodomain 1 0.045646 2.753182 ILMN_2129927 EXT1 exostosin glycosyltransferase 1 0.032789 2.737596 ILMN_1778599 SP140 SP140 nuclear body protein 0.049059 2.733013 ILMN_1760121 RRAGC Ras-related GTP binding C 0.043188 2.728264 Supplementary Table 2 (contd). List of genes downregulated in Treg-DC compared to mat-DC Probeset ID Gene symbol Description adj.P.Val Fold-change (mat-DC: Treg-DC) ILMN_1664776 EFR3A EFR3 homolog A (S. cerevisiae) 0.043036 2.723558 ILMN_3234089 N4BP2L2 NEDD4 binding protein 2-like 2 0.031298 2.719300 ILMN_1669881 TSPAN13 tetraspanin 13 0.048216 2.718616 ILMN_1723211 L2HGDH L-2-hydroxyglutarate dehydrogenase 0.042418 2.697199 ILMN_1700831 SLC27A2 solute carrier family 27 (fatty acid transporter), member 2 0.037541
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