Lee et al., Suppl. Fig. 1

Lee et al., Supplementary Table 1 Markers Percentage of p75+ cells [Mean ± SD] CD29 97.1 ± 2.5 CD133 65.3 ± 15 CD49d 75.3 ± 5 CD49b 67.4 ± 19 CXCR4 67.1 ± 12 CD73 3 ± 0.6 O4 1.9 ± 1 CD44 1.6 ± N/A CD45 0.2 ± N/A CD106 0 ± 0

Lee et al., Supplementary Table 2 p75+/hnk1+ p75-/hnk1- Differentiatial Expression FC >= 2 pval Gene Signal Detection Signal Detection Signal Fold Change Statistic 211341_at POU4F1 271 P 7 A 5 32.00 I 0.005% 210432_s_at SCN3A 131 P 3 A 4.6 24.25 I 0.003% 214451_at TFAP2B 3765 P 151 P 4.3 19.70 I 0.002% 209842_at SOX10 1806 P 118 A 4.1 17.15 I 0.002% 201131_s_at CDH1 74 P 6 A 4 16.00 I 0.035% 202454_s_at ERBB3 1929 P 168 P 3.6 12.13 I 0.002% 219054_at C5orf23 1011 P 116 P 3.6 12.13 I 0.015% 207145_at GDF8 244 P 22 P 3.4 10.56 I 0.002% 209200_at MEF2C 266 P 7 A 3.4 10.56 I 0.002% 207680_x_at PAX3 442 P 44 A 3.1 8.57 I 0.006% 204697_s_at CHGA 615 P 92 A 3 8.00 I 0.005% 209955_s_at FAP 361 P 45 A 3 8.00 I 0.004% 211896_s_at DCN 856 P 131 P 3 8.00 I 0.010% 205524_s_at HAPLN1 492 P 47 A 2.9 7.46 I 0.002% 205884_at ITGA4 95 P 8 A 2.9 7.46 I 0.003% 205113_at NEF3 3523 P 638 P 2.8 6.96 I 0.002% 205858_at NGFR 300 P 47 A 2.8 6.96 I 0.011% 214457_at HOXA2 479 P 50 A 2.8 6.96 I 0.077% 219789_at NPR3 284 P 59 A 2.8 6.96 I 0.007% 201506_at TGFBI 2175 P 427 P 2.5 5.66 I 0.002% 200872_at S100A10 873 P 195 A 2.3 4.92 I 0.002% 202950_at CRYZ 470 P 127 A 2.3 4.92 I 0.002% 204464_s_at EDNRA 1755 P 335 P 2.3 4.92 I 0.002% 205350_at CRABP1 13571 P 2340 P 2.3 4.92 I 0.002% 213139_at SNAI2 1577 P 313 P 2.3 4.92 I 0.002% 214218_s_at XIST 386 P 41 A 2.3 4.92 I 0.010% 216235_s_at EDNRA 574 P 92 A 2.3 4.92 I 0.002% 204471_at GAP43 1275 P 251 P 2.2 4.59 I 0.002% 204653_at TFAP2A 2328 P 439 P 2.2 4.59 I 0.002% 204654_s_at TFAP2A 867 P 148 P 2.2 4.59 I 0.002% 206935_at PCDH8 440 P 97 P 2.2 4.59 I 0.004% 207009_at PHOX2B 657 P 148 A 2.2 4.59 I 0.019% 210762_s_at DLC1 727 P 180 A 2.2 4.59 I 0.010% 214632_at NRP2 261 P 57 A 2.2 4.59 I 0.021% 201893_x_at DCN 1707 P 426 P 2.1 4.29 I 0.002% 202508_s_at SNAP25 335 P 85 P 2.1 4.29 I 0.062% 204239_s_at NNAT 1595 P 212 A 2.1 4.29 I 0.002% 212396_s_at KIAA0090 193 P 31 A 2.1 4.29 I 0.024% 213416_at ITGA4 375 P 121 A 2.1 4.29 I 0.003% 214803_at --- 2110 P 486 P 2.1 4.29 I 0.002% 211813_x_at DCN 1378 P 315 M 2 4.00 I 0.003% 221728_x_at XIST 450 P 94 A 2 4.00 I 0.017% 203423_at RBP1 2658 P 570 P 1.9 3.73 I 0.002%

Lee et al., Supplementary Table 2 204463_s_at EDNRA 333 P 101 M 1.9 3.73 I 0.003% 205150_s_at KIAA0644 1843 P 448 P 1.9 3.73 I 0.002% 205453_at HOXB2 1733 P 474 A 1.9 3.73 I 0.024% 206898_at CDH19 209 P 70 P 1.9 3.73 I 0.024% 209506_s_at NR2F1 2520 P 715 P 1.9 3.73 I 0.003% 209723_at SERPINB9 681 P 203 A 1.9 3.73 I 0.002% 209875_s_at SPP1 298 P 90 A 1.9 3.73 I 0.013% 202575_at CRABP2 6579 P 1229 P 1.8 3.48 I 0.002% 205533_s_at CDH6 96 P 32 A 1.8 3.48 I 0.019% 211651_s_at LAMB1 946 P 275 P 1.8 3.48 I 0.002% 215686_x_at TFAP2B 402 P 61 A 1.8 3.48 I 0.024% 216963_s_at GAP43 1363 P 292 M 1.8 3.48 I 0.004% 47550_at LZTS1 284 P 110 A 1.8 3.48 I 0.007% 202403_s_at COL1A2 8720 P 3025 P 1.7 3.25 I 0.002% 205433_at BCHE 1497 P 373 P 1.7 3.25 I 0.002% 206332_s_at IFI16 174 P 68 P 1.7 3.25 I 0.055% 213438_at NFASC 363 P 141 P 1.7 3.25 I 0.024% 200660_at S100A11 800 P 214 A 1.6 3.03 I 0.009% 201105_at LGALS1 1853 P 355 P 1.6 3.03 I 0.002% 201505_at LAMB1 829 P 257 P 1.6 3.03 I 0.002% 201744_s_at LUM 1833 P 609 P 1.6 3.03 I 0.002% 203001_s_at STMN2 5038 P 1650 P 1.6 3.03 I 0.002% 203789_s_at SEMA3C 651 P 169 P 1.6 3.03 I 0.002% 205430_at BMP5 242 P 66 A 1.6 3.03 I 0.011% 205528_s_at RUNX1T1 280 P 117 P 1.6 3.03 I 0.002% 218087_s_at SORBS1 251 P 70 P 1.6 3.03 I 0.004% 219106_s_at KBTBD10 99 P 18 A 1.6 3.03 I 0.005% 201163_s_at IGFBP7 223 P 48 A 1.5 2.83 I 0.011% 203424_s_at IGFBP5 912 P 277 P 1.5 2.83 I 0.002% 204646_at DPYD 133 P 34 M 1.5 2.83 I 0.011% 206424_at CYP26A1 1072 P 302 P 1.5 2.83 I 0.019% 209121_x_at NR2F2 2955 P 1657 P 1.5 2.83 I 0.008% 213385_at CHN2 506 P 251 P 1.5 2.83 I 0.005% 215228_at NHLH2 1041 P 413 P 1.5 2.83 I 0.002% 218409_s_at DNAJC1 1676 P 608 P 1.5 2.83 I 0.002% 219196_at SCG3 108 P 30 A 1.5 2.83 I 0.055% 219823_at LIN28 3130 P 1230 P 1.5 2.83 I 0.002% 202404_s_at COL1A2 4200 P 2668 P 1.4 2.64 I 0.002% 204948_s_at FST 1260 P 435 P 1.4 2.64 I 0.009% 205374_at SLN 457 P 168 A 1.4 2.64 I 0.005% 205805_s_at ROR1 763 P 291 P 1.4 2.64 I 0.003% 206135_at ST18 271 P 60 P 1.4 2.64 I 0.003% 207987_s_at GNRH1 135 P 49 A 1.4 2.64 I 0.013% 211959_at IGFBP5 3519 P 1224 P 1.4 2.64 I 0.002% 212099_at RHOB 3296 P 1515 P 1.4 2.64 I 0.002%

Lee et al., Supplementary Table 2 213601_at SLIT1 1136 P 519 P 1.4 2.64 I 0.002% 218589_at P2RY5 886 P 292 P 1.4 2.64 I 0.017% 219179_at DACT1 639 P 213 P 1.4 2.64 I 0.002% 221805_at NEFL 1187 P 451 P 1.4 2.64 I 0.002% 221916_at NEFL 1964 P 820 P 1.4 2.64 I 0.005% 201341_at ENC1 5147 P 1978 P 1.3 2.46 I 0.002% 201952_at ALCAM 988 P 368 P 1.3 2.46 I 0.002% 202947_s_at GYPC 1014 P 639 P 1.3 2.46 I 0.007% 203000_at STMN2 5957 P 2376 P 1.3 2.46 I 0.002% 205431_s_at BMP5 489 P 180 P 1.3 2.46 I 0.005% 205475_at SCRG1 771 P 268 P 1.3 2.46 I 0.006% 205885_s_at ITGA4 116 P 37 A 1.3 2.46 I 0.024% 207233_s_at MITF 461 P 114 A 1.3 2.46 I 0.013% 209708_at MOXD1 892 P 386 P 1.3 2.46 I 0.004% 210139_s_at PMP22 590 P 261 P 1.3 2.46 I 0.002% 213436_at CNR1 257 P 95 P 1.3 2.46 I 0.013% 213543_at --- 198 P 81 A 1.3 2.46 I 0.097% 213905_x_at BGN /// TS 625 P 229 P 1.3 2.46 I 0.006% 213921_at SST 1143 P 444 P 1.3 2.46 I 0.010% 215076_s_at COL3A1 1288 P 484 P 1.3 2.46 I 0.003% 219474_at C3orf52 246 P 101 A 1.3 2.46 I 0.002% 221269_s_at SH3BGRL3 1511 P 649 P 1.3 2.46 I 0.002% 221790_s_at LDLRAP1 244 P 89 A 1.3 2.46 I 0.021% 200704_at LITAF 1942 P 851 P 1.2 2.30 I 0.002% 200760_s_at ARL6IP5 3145 P 1289 P 1.2 2.30 I 0.002% 201012_at ANXA1 150 P 90 P 1.2 2.30 I 0.005% 203300_x_at AP1S2 1876 P 907 P 1.2 2.30 I 0.019% 203603_s_at ZFHX1B 271 P 144 P 1.2 2.30 I 0.007% 204850_s_at DCX 3811 P 2205 P 1.2 2.30 I 0.002% 205388_at TNNC2 330 P 138 A 1.2 2.30 I 0.005% 205532_s_at CDH6 638 P 237 P 1.2 2.30 I 0.006% 207345_at FST 338 P 121 P 1.2 2.30 I 0.002% 207871_s_at ST7 175 P 107 A 1.2 2.30 I 0.017% 208966_x_at IFI16 267 P 120 A 1.2 2.30 I 0.049% 209505_at NR2F1 5390 P 2371 P 1.2 2.30 I 0.002% 209840_s_at LRRN3 441 P 196 A 1.2 2.30 I 0.044% 209841_s_at LRRN3 858 P 269 P 1.2 2.30 I 0.002% 215045_at TNRC4 393 P 180 P 1.2 2.30 I 0.055% 215073_s_at NR2F2 505 P 218 P 1.2 2.30 I 0.077% 218072_at COMMD9 398 P 198 A 1.2 2.30 I 0.062% 221701_s_at STRA6 596 P 222 A 1.2 2.30 I 0.015% 200678_x_at GRN 1889 P 833 P 1.1 2.14 I 0.010% 201167_x_at ARHGDIA 244 P 148 M 1.1 2.14 I 0.015% 201469_s_at SHC1 438 P 213 P 1.1 2.14 I 0.055% 201578_at PODXL 896 P 416 P 1.1 2.14 I 0.035%

Lee et al., Supplementary Table 2 201852_x_at COL3A1 1136 P 556 P 1.1 2.14 I 0.013% 202599_s_at NRIP1 1950 P 1226 P 1.1 2.14 I 0.003% 203642_s_at COBLL1 329 P 99 P 1.1 2.14 I 0.062% 204044_at QPRT 1417 P 720 P 1.1 2.14 I 0.003% 204465_s_at INA 1321 P 604 P 1.1 2.14 I 0.021% 204584_at L1CAM 408 P 190 P 1.1 2.14 I 0.002% 205932_s_at MSX1 1382 P 616 P 1.1 2.14 I 0.006% 207558_s_at PITX2 69 P 37 A 1.1 2.14 I 0.013% 209361_s_at PCBP4 1930 P 1511 P 1.1 2.14 I 0.062% 210457_x_at HMGA1 514 P 253 P 1.1 2.14 I 0.009% 210809_s_at POSTN 564 P 232 P 1.1 2.14 I 0.049% 212419_at C10orf56 1161 P 382 P 1.1 2.14 I 0.013% 212423_at C10orf56 578 P 287 P 1.1 2.14 I 0.015% 212865_s_at COL14A1 76 P 40 A 1.1 2.14 I 0.027% 217996_at PHLDA1 363 P 163 P 1.1 2.14 I 0.005% 218231_at NAGK 680 P 383 A 1.1 2.14 I 0.049% 219615_s_at KCNK5 539 P 224 P 1.1 2.14 I 0.024% 219955_at L1TD1 1442 P 822 P 1.1 2.14 I 0.004% 58308_at TRIM62 171 P 99 A 1.1 2.14 I 0.050% 200696_s_at GSN 1118 P 482 P 1 2.00 I 0.006% 200761_s_at ARL6IP5 4057 P 3003 P 1 2.00 I 0.019% 201204_s_at RRBP1 538 P 215 P 1 2.00 I 0.027% 201261_x_at BGN 515 P 206 P 1 2.00 I 0.035% 201951_at ALCAM 119 P 50 A 1 2.00 I 0.062% 203131_at PDGFRA 801 P 336 P 1 2.00 I 0.002% 203295_s_at ATP1A2 1043 P 464 P 1 2.00 I 0.044% 203973_s_at CEBPD 186 P 67 A 1 2.00 I 0.077% 204151_x_at AKR1C1 824 P 438 P 1 2.00 I 0.002% 204540_at EEF1A2 744 P 254 P 1 2.00 I 0.024% 204743_at TAGLN3 2369 P 1002 P 1 2.00 I 0.004% 205375_at MDFI 673 P 516 P 1 2.00 I 0.062% 208540_x_at S100A11 680 P 398 P 1 2.00 I 0.031% 209119_x_at NR2F2 614 P 349 P 1 2.00 I 0.006% 209120_at NR2F2 2703 P 1314 P 1 2.00 I 0.002% 209914_s_at NRXN1 258 P 116 A 1 2.00 I 0.002% 210602_s_at CDH6 758 P 326 P 1 2.00 I 0.002% 212484_at FAM89B 857 P 358 A 1 2.00 I 0.055% 213094_at GPR126 115 P 47 A 1 2.00 I 0.002% 214628_at NHLH1 921 P 476 P 1 2.00 I 0.002% 216041_x_at GRN 1006 P 729 P 1 2.00 I 0.003% 219147_s_at C9orf95 206 P 111 P 1 2.00 I 0.006% 219167_at RASL12 517 P 199 A 1 2.00 I 0.021% 219315_s_at C16orf30 430 P 159 P 1 2.00 I 0.005% 220116_at KCNN2 106 P 54 A 1 2.00 I 0.077% 220551_at SLC17A6 335 P 200 P 1 2.00 I 0.006%

Lee et al., Supplementary Table 2 221236_s_at STMN4 1134 P 493 P 1 2.00 I 0.007% 221773_at ELK3 427 P 186 P 1 2.00 I 0.003% 221801_x_at NEFL 242 P 152 A 1 2.00 I 0.031% 200897_s_at PALLD 2632 P 4605 P -1-2.00 D 0.002% 202043_s_at SMS 1554 P 3279 P -1-2.00 D 0.002% 202206_at ARL4C 2003 P 3864 P -1-2.00 D 0.002% 202581_at HSPA1B 541 P 1160 P -1-2.00 D 0.004% 202761_s_at SYNE2 1314 P 2717 P -1-2.00 D 0.002% 202823_at TCEB1 224 P 443 P -1-2.00 D 0.003% 202965_s_at CAPN6 627 P 1249 P -1-2.00 D 0.003% 202966_at CAPN6 291 P 487 P -1-2.00 D 0.077% 203243_s_at PDLIM5 303 P 775 P -1-2.00 D 0.027% 203409_at DDB2 1081 P 2182 P -1-2.00 D 0.005% 203413_at NELL2 1976 P 4090 P -1-2.00 D 0.002% 203499_at EPHA2 440 P 926 P -1-2.00 D 0.021% 203685_at BCL2 230 P 372 P -1-2.00 D 0.015% 204288_s_at SORBS2 269 P 630 P -1-2.00 D 0.049% 204304_s_at PROM1 736 P 1361 P -1-2.00 D 0.002% 204391_x_at TRIM24 1599 P 3391 P -1-2.00 D 0.004% 204823_at NAV3 355 A 726 P -1-2.00 D 0.005% 205413_at MPPED2 378 P 643 P -1-2.00 D 0.010% 207547_s_at FAM107A 256 P 573 P -1-2.00 D 0.005% 208783_s_at CD46 840 P 1716 P -1-2.00 D 0.002% 209140_x_at HLA-B 2314 P 5655 P -1-2.00 D 0.002% 209189_at FOS 1797 P 3823 P -1-2.00 D 0.003% 209560_s_at DLK1 14847 P 32913 P -1-2.00 D 0.002% 210095_s_at IGFBP3 340 P 688 P -1-2.00 D 0.002% 210592_s_at SAT 1935 P 3531 P -1-2.00 D 0.002% 210611_s_at DTNA 82 M 183 P -1-2.00 D 0.087% 212811_x_at SLC1A4 221 P 435 P -1-2.00 D 0.087% 213110_s_at COL4A5 2055 P 3614 P -1-2.00 D 0.002% 213293_s_at TRIM22 212 P 358 P -1-2.00 D 0.006% 213994_s_at SPON1 87 P 263 P -1-2.00 D 0.039% 214238_at --- 199 P 249 P -1-2.00 D 0.031% 215692_s_at MPPED2 207 P 343 P -1-2.00 D 0.013% 216733_s_at GATM 143 P 391 P -1-2.00 D 0.062% 217130_at C9orf33 140 M 302 P -1-2.00 D 0.007% 219938_s_at PSTPIP2 130 P 240 P -1-2.00 D 0.017% 200606_at DSP 393 P 993 P -1.1-2.14 D 0.008% 200907_s_at PALLD 913 P 2220 P -1.1-2.14 D 0.004% 202207_at ARL4C 1683 P 3507 P -1.1-2.14 D 0.002% 202208_s_at ARL4C 800 P 2110 P -1.1-2.14 D 0.011% 202458_at PRSS23 776 P 1304 P -1.1-2.14 D 0.002% 204011_at SPRY2 1407 P 2658 P -1.1-2.14 D 0.002% 204165_at WASF1 1398 P 3053 P -1.1-2.14 D 0.019%

Lee et al., Supplementary Table 2 204573_at CROT 344 P 851 P -1.1-2.14 D 0.002% 205103_at C1orf61 944 P 2809 P -1.1-2.14 D 0.010% 206373_at ZIC1 6437 P 14922 P -1.1-2.14 D 0.003% 208812_x_at HLA-C 2604 P 4340 P -1.1-2.14 D 0.002% 208892_s_at DUSP6 962 P 2031 P -1.1-2.14 D 0.004% 209295_at TNFRSF10 1222 P 2869 P -1.1-2.14 D 0.004% 209590_at BMP7 662 P 1067 P -1.1-2.14 D 0.005% 209897_s_at SLIT2 739 P 1529 P -1.1-2.14 D 0.002% 211219_s_at LHX2 682 P 1835 P -1.1-2.14 D 0.002% 212636_at QKI 592 P 1707 P -1.1-2.14 D 0.002% 213134_x_at BTG3 1112 P 3156 P -1.1-2.14 D 0.002% 213301_x_at TRIM24 1167 P 2435 P -1.1-2.14 D 0.002% 213992_at COL4A6 2809 P 5357 P -1.1-2.14 D 0.002% 214183_s_at TKTL1 140 A 302 P -1.1-2.14 D 0.005% 215268_at KIAA0754 88 A 167 P -1.1-2.14 D 0.044% 218437_s_at LZTFL1 427 P 798 P -1.1-2.14 D 0.002% 218602_s_at FAM29A 93 P 125 P -1.1-2.14 D 0.021% 218902_at NOTCH1 625 P 1286 P -1.1-2.14 D 0.004% 219301_s_at CNTNAP2 736 P 1379 P -1.1-2.14 D 0.017% 219522_at FJX1 476 P 920 P -1.1-2.14 D 0.035% 219628_at WIG1 496 P 966 P -1.1-2.14 D 0.002% 219693_at AGPAT4 335 P 816 P -1.1-2.14 D 0.006% 221683_s_at CEP290 79 P 175 P -1.1-2.14 D 0.021% 221950_at EMX2 1805 P 4836 P -1.1-2.14 D 0.004% 201185_at HTRA1 414 P 928 P -1.2-2.30 D 0.005% 201842_s_at EFEMP1 420 P 1217 P -1.2-2.30 D 0.002% 202177_at GAS6 213 A 387 P -1.2-2.30 D 0.049% 203881_s_at DMD 453 P 1033 P -1.2-2.30 D 0.002% 203988_s_at FUT8 360 P 835 P -1.2-2.30 D 0.017% 205543_at HSPA4L 146 A 344 P -1.2-2.30 D 0.003% 206140_at LHX2 3427 P 8390 P -1.2-2.30 D 0.002% 207067_s_at HDC 336 A 768 P -1.2-2.30 D 0.006% 209763_at CHRDL1 331 P 676 P -1.2-2.30 D 0.019% 209917_s_at TP53AP1 410 P 821 P -1.2-2.30 D 0.002% 210281_s_at ZNF198 267 P 533 P -1.2-2.30 D 0.039% 212096_s_at MTUS1 232 P 574 P -1.2-2.30 D 0.003% 212526_at SPG20 239 P 694 P -1.2-2.30 D 0.002% 214459_x_at HLA-C 1989 P 3698 P -1.2-2.30 D 0.006% 214633_at SOX3 1181 P 2922 P -1.2-2.30 D 0.002% 217519_at MACF1 45 P 107 P -1.2-2.30 D 0.044% 218298_s_at C14orf159 323 P 528 P -1.2-2.30 D 0.004% 218885_s_at GALNT12 901 P 1148 P -1.2-2.30 D 0.003% 219300_s_at CNTNAP2 660 P 1025 P -1.2-2.30 D 0.007% 219415_at TTYH1 1142 P 2640 P -1.2-2.30 D 0.002% 219871_at FLJ13197 124 P 346 P -1.2-2.30 D 0.031%

Lee et al., Supplementary Table 2 219895_at FAM70A 222 P 558 P -1.2-2.30 D 0.002% 222018_at NACA /// N 203 P 363 P -1.2-2.30 D 0.010% 203178_at GATM 106 P 125 P -1.3-2.46 D 0.005% 203904_x_at CD82 484 A 1103 P -1.3-2.46 D 0.044% 205229_s_at COCH 365 P 781 P -1.3-2.46 D 0.002% 210282_at ZNF198 173 P 262 P -1.3-2.46 D 0.015% 215717_s_at FBN2 153 P 384 P -1.3-2.46 D 0.003% 220987_s_at C11orf17 // 518 P 1403 P -1.3-2.46 D 0.002% 222316_at VDP 61 P 189 P -1.3-2.46 D 0.009% 36711_at MAFF 132 P 359 P -1.3-2.46 D 0.004% 201843_s_at EFEMP1 55 A 154 P -1.4-2.64 D 0.002% 201939_at PLK2 205 P 460 P -1.4-2.64 D 0.003% 204160_s_at ENPP4 73 A 246 P -1.4-2.64 D 0.024% 204724_s_at COL9A3 178 A 606 P -1.4-2.64 D 0.010% 207943_x_at PLAGL1 332 P 837 P -1.4-2.64 D 0.005% 210394_x_at SSX4 /// SS 67 A 304 P -1.4-2.64 D 0.019% 214046_at --- 577 P 1471 P -1.4-2.64 D 0.002% 215145_s_at CNTNAP2 449 P 1142 P -1.4-2.64 D 0.015% 220795_s_at KIAA1446 259 A 483 P -1.4-2.64 D 0.044% 221029_s_at WNT5B 427 P 1043 P -1.4-2.64 D 0.002% 203349_s_at ETV5 371 P 1112 P -1.5-2.83 D 0.002% 205931_s_at CREB5 166 A 303 P -1.5-2.83 D 0.007% 206018_at FOXG1B 3051 P 12892 P -1.5-2.83 D 0.004% 211479_s_at HTR2C 43 P 111 P -1.5-2.83 D 0.006% 212977_at CMKOR1 432 P 1195 P -1.5-2.83 D 0.002% 215469_at --- 48 A 153 P -1.5-2.83 D 0.015% 220014_at LOC51334 75 P 189 P -1.5-2.83 D 0.006% 204285_s_at PMAIP1 221 P 751 P -1.6-3.03 D 0.002% 207002_s_at PLAGL1 246 P 842 P -1.6-3.03 D 0.003% 208893_s_at DUSP6 439 M 1362 P -1.6-3.03 D 0.027% 213482_at DOCK3 59 A 162 P -1.6-3.03 D 0.031% 221577_x_at GDF15 133 A 390 P -1.6-3.03 D 0.010% 201005_at CD9 154 P 576 P -1.7-3.25 D 0.004% 205029_s_at FABP7 2087 P 7288 P -1.7-3.25 D 0.002% 205030_at FABP7 5281 P 14660 P -1.7-3.25 D 0.002% 207658_s_at FOXG1B // 365 P 1834 P -1.7-3.25 D 0.004% 209301_at CA2 451 P 1442 P -1.7-3.25 D 0.002% 209318_x_at PLAGL1 412 P 1169 P -1.7-3.25 D 0.002% 209504_s_at PLEKHB1 304 P 907 P -1.7-3.25 D 0.003% 210037_s_at NOS2A 139 P 428 P -1.7-3.25 D 0.006% 221086_s_at ZNF312 719 P 1238 P -1.7-3.25 D 0.005% 202023_at EFNA1 105 A 434 P -1.8-3.48 D 0.006% 204712_at WIF1 83 P 266 P -1.8-3.48 D 0.009% 206349_at LGI1 381 P 1485 P -1.8-3.48 D 0.002% 206634_at SIX3 603 P 1465 P -1.8-3.48 D 0.011%

Lee et al., Supplementary Table 2 208498_s_at AMY1A /// A 19 A 98 P -1.8-3.48 D 0.062% 214078_at PAK3 149 P 520 P -1.8-3.48 D 0.002% 222325_at RMST 483 P 1425 P -1.8-3.48 D 0.002% 207307_at HTR2C 153 P 473 P -1.9-3.73 D 0.002% 213880_at LGR5 192 P 680 P -1.9-3.73 D 0.002% 205442_at MFAP3L 41 A 188 P -2-4.00 D 0.002% 204286_s_at PMAIP1 76 P 308 P -2.1-4.29 D 0.035% 207267_s_at DSCR6 76 P 483 P -2.1-4.29 D 0.005% 212558_at SPRY1 492 P 1916 P -2.1-4.29 D 0.002% 210729_at NPY2R 52 P 200 P -2.3-4.92 D 0.005% 219313_at GRAMD1C 36 A 122 P -2.4-5.28 D 0.021% 209074_s_at FAM107A 49 A 448 P -2.7-6.50 D 0.004% 221245_s_at C2orf31 352 P 2590 P -2.7-6.50 D 0.002% 221376_at FGF17 44 A 430 P -2.8-6.96 D 0.055% 204363_at F3 30 A 283 P -3-8.00 D 0.011% 219171_s_at ZNF236 7 A 107 P -3.7-13.00 D 0.005% 208449_s_at FGF8 5 A 124 P -3.9-14.93 D 0.039% 220269_at FLJ23049 6 A 144 P -4.1-17.15 D 0.019%

Lee et al., Supplementary Table 3 Name COMPANY Name COMPANY AFP Sigma Lyve-1 Chemicon AP2b DSHB MBP Chemicon Alpha2 integrin (CD49b)-PE BD Musashi1 R&D Alpha4 integrin (CD49d)-PE BD NCAM (eric-1) SCBT ALP (Bone-specific) DSHB NCAM (5.1H11) DSHB Brn3a Chemicon NG2 Chemicon Calponin Sigma Nestin R&D CD105-PE AbDSerotec O4 Chemicon CD106 (V-CAM) APC BD Oct-4 SCBT CD133-PE Miltenyi p75 Advanced targeting system CD146-PE BD Pax6 DSHB CD29-PEcy5 BD PCNA Sigma CD44-PE BD Peripherin Abcam Chemicon CD45-PE BD S100 DAKO CD73-PE BD SM22a Vision Bio Collagen II Chondrex SMA Sigma CXCR4 BD Sox10 Sigma DBH Pel-Freez Sox2 SCBT GABA Sigma SSEA-4 DSHB GFAP MP biomedical Stro1 SCBT Human nuclear antigen Chemicon TH Pel-Freez Hnk1 Sigma Tuj1 Covance Islet1 DSHB Vimentin-cy3 Sigma Ki-67 Sigma

Lee et al., Supplementary Table 4 Name Orientation Ann. Tem Size Sequence Aggrecan Sense 56 190 CACTGTTACCGCCACTTCCC ACCAGCGGAAGTCCCCTTCG ALP Sense 51 454 TGGAGCTTCAGAAGCTCAACACCA ATCTCGTTGTCTGAGTACCAGTCC Ap2 Sense 50 396 TCCCTGTCCAAGTCCAACAGCAAT AAATTCGGTTTCGCACACGTACCC BSP Sense 56 450 AATGAAAACGAAGAAAGCGAAG ATCATAGCCATCGTAGCCTTGT ChgA Sense 60 265 AACCAGAGCAGCCAGGCCGAG TGGCTGGAGGGTGGGTGTTGG Collagen2 Sense 58 390 ATGATTCGCCTCGGGGCTCC CATTACTGGGAACTGGGCGC ENDRA Sense 56 252 TATCAATGTATTTAAGCTGCTGG GGAATGGCCAGGATAAAGG ErbB3 Sense 57 365 GGTGCTGGGCTTGCTTTT CGTGGCTGGAGTTGGTGTTA GAPDH Sense 59 342 CCCCTTCATTGACCTCAACTACA TTGCTGATGATCTTGAGGCTGT HoxA2 Sense 58 267 TACCCCTGGATGAAGGAGAAG AGTCAAATCCAGCAGCGCTG Msx-1 Sense 59 284 CCTTCCCTTTAACCCTCACAC CCGATTTCTCTGCGCTTTTCT Oct3/4 Sense 55 422 ATTTGCCAAGCTCCTGAAGCAG TTGATCGCTTGCCCTTCTGG Pax3 Sense 60 349 GCACTGTACACCAAAGCACG TAGGTGGGTGGACAGTAGGA PPARγ Sense 56 350 CTCCTATTGACCCAGAAAGC GTAGAGCTGAGTCTTCTCAG SCN3a Sense 56 240 GTAGTGGTGCATTGGCCTTT GCACCGAGTTCTGAGTAGCC Slug Sense 58 410 AGCGAACTGGACACACATAC TCTAGACTGGGCATCGCAG SmMActin α sense 54 205 CTGTTTTCCCATCCATTGTGG antisense GCAACACGAAGCTCATTGTAG SmMActin γ sense 56 245 TGGCACCACTCCTTCTACAATG antisense TCATAGATGGGGACATTGTGG Snail Sense 53 611 CTCCTCTACTTCAGCCTCTT CTTCATCAAAGTCCTGTGGG Sox10 Sense 61 250 ATACGACACTGTCCCGGCCCTAAA TTCTCCTCTGTCCAGCCTGTTCTC