RARα2 expression confers myeloma stem cell features Ye Yang, Jumei Shi, Giulia Tolomelli, Hongwei Xu, Jiliang Xia, He Wang, Wen Zhou, Yi Zhou, Satyabrata Das, Zhimin Gu, Dana Levasseur, Fenghuang Zhan, and Guido Tricot Supplemental Data Table S1, related to Figure 1. Supplemental Experimental Procedures
Supplemental Data Table S1: Differentially Expressed Genes between CD138 + with CD138 - MM Cells Probe Set Name Gene Symbol Chromosomal Location CD138 + CD138 - p ttest CD138 - /CD138 + 240988_x_at --- --- 9.3 684.7 0.000547 73.80 231597_x_at --- --- 433.9 11053.0 0.000239 25.47 1565358_at RARA chr17q21 68.5 1592.0 0.000972 23.23 243489_at --- --- 107.4 1980.5 0.000633 18.45 211565_at SH3GL3 chr15q24 60.8 1028.2 0.000647 16.92 1560144_at --- --- 39.4 561.3 0.000752 14.25 1561346_at --- --- 104.2 1079.7 0.002203 10.36 225767_at --- --- 767.1 7446.7 0.004875 9.71 215599_at LOC730390 /// SMA4 chr5q13 163.2 1508.4 0.000808 9.24 1558048_x_at --- --- 880.3 8038.6 5.27E-05 9.13 1562527_at LOC283027 chr10q11.1 67.1 579.5 0.00535 8.64 225762_x_at LOC284801 chr20p11.1 238.9 1925.2 0.003377 8.06 220232_at SCD5 chr4q21.22 351.7 2586.7 0.001401 7.36 234675_x_at --- --- 5694.1 41312.0 0.000643 7.26 224159_x_at TRIM4 chr7q22-q31.1 584.8 4139.6 0.000883 7.08 242862_x_at --- --- 298.2 2067.4 0.001594 6.93 222145_at --- --- 77.6 511.9 0.008107 6.60 81737_at --- --- 78.2 509.5 0.000556 6.51 234762_x_at NLN chr5q12.3 852.7 5448.2 0.001647 6.39 236856_x_at --- --- 126.0 800.2 0.003468 6.35 216858_x_at --- --- 465.3 2718.6 0.000819 5.84 234723_x_at --- --- 469.3 2740.5 0.001899 5.84 1570255_s_at ANKRD20A1 /// chr2q11.1 /// 95.6 551.7 0.009807 5.77 234562_x_at LOC728678 /// LOC731914 chr3p22.3 167.3 963.9 0.008476 5.76 220691_at --- --- 96.3 549.8 0.002514 5.71 232964_at LOC442590 /// WBSCR19 chr7p13 /// chr7q11.23 175.9 906.6 0.008071 5.15 214715_x_at ZNF160 chr19q13.41 1194.1 6030.9 0.003386 5.05 1566887_x_at --- --- 468.2 2348.2 0.003909 5.02 210686_x_at SLC25A16 chr10q21.3 713.5 3527.7 0.000899 4.94 224254_x_at --- --- 327.2 1607.1 0.003513 4.91 220796_x_at SLC35E1 chr19p13.11 1281.8 6245.4 0.005923 4.87 235190_at --- --- 569.8 2701.9 0.006034 4.74 214372_x_at ERN2 chr16p12.2 110.6 514.3 0.000487 4.65 1563483_at FAM91A2 chr1q21.1 140.0 643.3 0.001968 4.60 237868_x_at --- --- 176.7 810.1 0.002265 4.59 242712_x_at RANBP2 /// chr2p11.2 /// 123.0 560.2 0.002713 4.55 216524_x_at --- --- 263.7 1156.6 0.005805 4.39 206323_x_at OPHN1 chrxq12 3090.0 13461.1 0.001151 4.36 238701_x_at FLJ45803 chr11q23.1 5061.5 22042.0 0.002764 4.35
206169_x_at ZC3H7B chr22q13.2 268.7 1157.8 0.000433 4.31 241223_x_at --- --- 343.1 1475.4 0.002008 4.30 216187_x_at --- --- 1635.1 6993.8 0.004765 4.28 215067_x_at PRDX2 chr19p13.2 169.5 713.1 0.00248 4.21 216153_x_at RECK chr9p13-p12 714.5 2995.3 0.001965 4.19 215604_x_at --- --- 382.7 1583.4 0.002723 4.14 214707_x_at ALMS1 chr2p13 312.2 1291.5 0.006169 4.14 242201_at PMS2L5 chr7q11-q22 463.3 1893.3 0.002385 4.09 233056_x_at DLGAP4 chr20q11.23 433.1 1737.9 0.008319 4.01 241632_x_at --- --- 169.7 680.5 0.005597 4.01 216859_x_at --- --- 148.5 582.4 0.001698 3.92 242369_x_at --- --- 137.7 537.2 0.002505 3.90 217679_x_at --- --- 916.7 3558.5 0.004841 3.88 233810_x_at PRO1268 --- 150.4 566.2 0.001616 3.77 233702_x_at --- --- 706.1 2645.7 0.004194 3.75 233427_x_at --- --- 199.4 743.0 0.007702 3.73 211454_x_at FKSG49 chr13q14.3 854.5 3167.7 0.006613 3.71 215179_x_at PGF chr14q24-q31 1210.2 4422.4 0.001579 3.65 223662_x_at DDX59 chr1q32.1 515.9 1883.7 0.006725 3.65 222380_s_at PDCD6 chr5pter-p15.2 140.0 510.9 0.000114 3.65 242961_x_at DDX58 chr9p12 159.0 567.4 0.009703 3.57 215600_x_at FBXW12 chr3p21.31 937.8 3329.0 0.00441 3.55 215628_x_at --- --- 459.5 1625.9 0.00223 3.54 242476_at --- --- 145.4 514.2 0.004728 3.54 237475_x_at SEPP1 chr5q31 1129.0 3947.5 0.008872 3.50 216051_x_at --- --- 209.0 727.1 0.002989 3.48 223781_x_at ADH4 chr4q21-q24 4q22 205.0 705.6 0.000312 3.44 215383_x_at SPG21 chr15q21-q22 535.1 1839.1 0.00104 3.44 232889_at GUSBP1 chr5q13.2 266.7 915.7 0.007751 3.43 233779_x_at --- --- 225.3 769.6 0.00314 3.42 220452_x_at IL17RA chr22q11.1 388.8 1321.4 0.006106 3.40 236715_x_at UACA chr15q22-q24 301.7 1006.0 0.006854 3.33 1566084_at LOC644215 chr10q24.1 187.9 623.8 0.001873 3.32 224429_x_at --- --- 295.8 962.2 0.002149 3.25 220725_x_at DNAH3 chr16p12.2 683.9 2218.8 0.005002 3.24 207365_x_at USP34 chr2p15 849.3 2749.6 0.009605 3.24 234341_x_at LOC91548 chr1q32.3 315.8 1015.4 0.007905 3.22 224667_x_at C10orf104 chr10q22.1 1076.1 3455.3 0.008349 3.21 208246_x_at --- --- 1278.2 4099.3 0.00515 3.21 217713_x_at --- --- 214.2 686.0 0.005474 3.20 214902_x_at --- --- 501.8 1606.1 0.004236 3.20 216229_x_at HCG2P7 chr6p21.3 169.7 539.0 0.005137 3.18 244495_x_at C18orf45 chr18q11.2 953.7 3001.2 0.00069 3.15 206792_x_at PDE4C chr19p13.11 1751.2 5492.2 0.004536 3.14 215588_x_at RIOK3 chr18q11.2 609.3 1907.7 0.006346 3.13 218750_at JOSD3 chr11q21 303.0 938.8 0.007183 3.10 1555878_at RPS24 chr10q22-q23 168.8 514.8 0.00121 3.05 232347_x_at --- --- 190.1 578.1 0.003474 3.04
234788_x_at --- --- 390.9 1185.5 0.008809 3.03 238893_at LOC338758 chr12q21.33 173.4 523.8 0.00318 3.02 239748_x_at OCIAD1 chr4p11 1678.9 5060.6 0.00541 3.01 214594_x_at ATP8B1 chr18q21- q22 18q21.31 494.9 1478.4 0.004753 2.99 1552729_at SNHG7 chr9q34.3 203.1 594.1 0.001589 2.92 241718_x_at --- --- 261.8 761.3 0.008056 2.91 242191_at NBPF10 /// NBPF11 chr1q21.1 296.1 861.1 0.00559 2.91 207046_at HIST2H4A /// HIST2H4B chr1q21 209.7 608.4 0.005571 2.90 244197_x_at --- --- 603.0 1749.8 0.004572 2.90 232597_x_at SFRS2IP chr12q13.11 375.0 1078.9 0.003524 2.88 232266_x_at CDC2L5 chr7p13 1693.8 4850.2 0.006488 2.86 223802_s_at RBBP6 chr16p12.2 399.1 1127.3 0.002261 2.82 208137_x_at LOC731901 chr19q13.41 665.3 1873.5 0.005709 2.82 233041_x_at --- --- 442.0 1232.8 0.003064 2.79 232169_x_at NDUFS8 chr11q13 408.9 1135.0 0.003808 2.78 242646_at --- --- 200.7 548.4 0.001788 2.73 211445_x_at NACAP1 chr8q22.3 2546.7 6914.6 0.003932 2.72 237768_x_at --- --- 220.5 598.5 0.007552 2.71 231825_x_at ATF7IP chr12p13.1 1073.7 2878.0 0.009601 2.68 215467_x_at LOC647070 chr1q25.3 218.9 576.4 0.006857 2.63 206056_x_at SPN chr16p11.2 513.2 1350.6 0.007389 2.63 240205_x_at --- --- 225.3 591.8 0.007715 2.63 215978_x_at LOC152719 chr4p16.3 1718.3 4509.6 0.004604 2.62 233775_x_at --- --- 423.2 1103.9 0.0026 2.61 229574_at TRA2A chr7p15.3 353.1 917.0 0.006004 2.60 217703_x_at --- --- 378.6 981.3 0.001268 2.59 1554595_at SYMPK chr19q13.3 238.0 616.2 0.000852 2.59 1557996_at POLR2J4 chr7p13 258.5 668.5 0.000335 2.59 207730_x_at --- --- 919.5 2360.9 0.005918 2.57 242438_at --- --- 348.2 892.7 0.006731 2.56 1559436_x_at --- --- 580.5 1475.9 0.007767 2.54 243318_at WDR42A chr1q22-q23 413.1 1022.7 0.009864 2.48 220113_x_at POLR1B chr2q13 337.0 832.0 0.006812 2.47 220720_x_at FAM128B chr2q21.1 298.3 729.2 0.004627 2.44 1559167_x_at MPV17L chr16p13.11 390.2 951.9 0.009884 2.44 236841_at FAM39DP chr15q26.3 551.8 1342.2 0.000378 2.43 215529_x_at DIP2A chr21q22.3 485.0 1174.5 0.00195 2.42 217704_x_at --- --- 265.8 643.6 0.009738 2.42 235084_x_at --- --- 319.8 772.8 0.007608 2.42 234981_x_at CMBL chr5p15.2 2143.0 5163.8 0.004357 2.41 208082_x_at --- --- 901.4 2156.8 0.003338 2.39 1552622_s_at LOC441259 chr7p13 384.1 916.6 0.004201 2.39 1568627_at SMEK2 chr2p16.1 214.4 501.4 0.000262 2.34 208238_x_at --- --- 565.4 1321.8 0.004793 2.34 217579_x_at --- --- 233.9 544.6 0.005006 2.33 235167_at DKFZp547E087 chr18p11.21 279.0 642.2 0.005263 2.30
225899_x_at FLJ45445 chr11p15.5 408.0 931.6 0.003025 2.28 211600_at --- --- 10700.4 24282.1 2.28E-05 2.27 222207_x_at LOC389517 chr7q11.23 737.6 1650.1 0.000765 2.24 238449_at LOC595101 chr16p11.2 393.5 879.4 0.003252 2.23 242195_x_at NUMBL chr19q13.13-q13.2 892.2 1983.4 0.00679 2.22 226663_at ANKRD10 chr13q34 442.2 982.5 0.008213 2.22 205370_x_at DBT chr1p31 2276.1 4926.7 0.007721 2.16 224517_at POLR2J4 chr7p13 260.1 558.0 0.001962 2.15 204387_x_at MRP63 --- 780.2 1658.3 0.004925 2.13 242550_at EIF3B chr7p22.2 302.5 616.1 0.000673 2.04 1570210_x_at SAPS2 chr22q13.33 279.4 567.2 0.002031 2.03 207436_x_at KIAA0894 chr10q23.33 690.8 1389.7 0.009848 2.01 60528_at PLA2G4B chr15q11.2-q21.3 305.1 609.1 0.006622 2.00 225035_x_at CXYorf1 chr15q26.3 870.5 1710.5 0.005047 1.96 1553718_at ZNF548 chr19q13.43 560.1 1090.6 0.007027 1.95 1556035_s_at ZNF207 chr17q11.2 444.2 864.3 0.002307 1.95 236836_at --- --- 278.2 541.2 0.007064 1.95 1557409_at --- --- 286.6 555.8 0.002161 1.94 231999_at ANKRD11 chr16q24.3 278.7 538.5 0.001762 1.93 235094_at --- --- 516.2 993.9 0.008382 1.93 217329_x_at --- --- 1895.3 3638.3 0.00622 1.92 228879_at --- --- 938.0 1791.3 0.007832 1.91 216309_x_at JRK chr8q24.3 298.5 568.6 0.009873 1.90 220352_x_at --- --- 334.2 636.0 0.009348 1.90 1556007_s_at CSNK1A1 chr5q32 299.8 568.8 0.00456 1.90 203419_at MLL4 chr19q13.1 417.2 788.8 0.007417 1.89 1555653_at HNRPA3 chr2q31.2 17696.4 33176.7 0.000582 1.87 238199_x_at LOC440552 chr1p36.33 3514.4 6505.6 7.77E-05 1.85 231992_x_at --- --- 316.5 563.8 0.009495 1.78 214870_x_at LOC339047 chr16p13-p11 2575.7 4568.5 0.009142 1.77 228930_at SCARNA15 chr15q25.2 442.6 771.9 0.007246 1.74 219577_s_at ABCA7 chr19p13.3 344.1 596.4 0.008636 1.73 216387_x_at LOC390411 chr13q21.33 623.9 1078.2 0.001596 1.73 1553551_s_at --- --- 51329.1 85251.2 0.004631 1.66 202281_at GAK chr4p16 701.4 1162.7 0.007566 1.66 225995_x_at FAM39B chr2q14.1 569.1 934.6 0.00152 1.64 218920_at FLJ10404 chr5q35.3 525.8 860.6 0.005143 1.64 242837_at SFRS4 chr1p35.3 320.6 519.6 0.007779 1.62 221501_x_at LOC339047 chr16p13.11 3782.9 6067.7 0.00917 1.60 58994_at CC2D1A chr19p13.12 322.5 510.3 0.005929 1.58 207435_s_at SRRM2 chr16p13.3 1093.5 1702.4 0.001414 1.56 216713_at KRIT1 chr7q21-q22 541.3 838.7 0.005253 1.55 203055_s_at ARHGEF1 chr19q13.13 494.9 763.6 0.007949 1.54 230598_at --- --- 356.5 545.8 0.00257 1.53 204275_at SOLH chr16p13.3 365.9 549.6 0.006364 1.50 232420_x_at LOC286260 chr9q34.3 427.2 637.4 0.0092 1.49 225393_at GATAD2B chr1q21.3 648.7 956.7 0.007372 1.47 227651_at BTBD14B chr19p13.13 816.3 1202.3 6.82E-05 1.47
218155_x_at TSR1 chr17p13.3 970.8 1419.2 0.007726 1.46 201480_s_at SUPT5H chr19q13 1099.5 1606.6 0.008352 1.46 214316_x_at --- --- 551.4 801.4 0.009022 1.45 218064_s_at AKAP8L chr19p13.12 797.6 1154.7 0.004885 1.45 238807_at ANKRD46 chr8q22.3 386.8 559.8 0.00241 1.45 221540_x_at DKFZP686M019 9 chr5q12.2-q13.3 1252.9 1812.0 0.003774 1.45 213065_at CCDC131 chr12q21.1 639.1 905.0 0.004012 1.42 217801_at ATP5E chr20q13.32 24016.5 33777.3 0.001048 1.41 211289_x_at CDC2L1 chr1p36.33 751.4 1056.4 0.008592 1.41 41657_at STK11 chr19p13.3 395.9 556.3 0.006553 1.41 218797_s_at LOC644124 chr17q25 695.4 959.6 0.007298 1.38 209411_s_at GGA3 chr17q25.1 563.0 770.5 0.00786 1.37 223203_at TMEM29 chrxp11.22 716.0 979.4 0.002105 1.37 201439_at GBF1 chr10q24 517.7 696.4 0.000801 1.35 225131_at ZRANB1 chr10q26.13 597.4 802.5 0.006587 1.34 210346_s_at CLK4 chr5q35 896.3 1203.5 0.007016 1.34 218524_at E4F1 chr16p13.3 394.6 529.8 0.005067 1.34 224977_at C6orf89 chr6p21.2 542.6 728.5 0.007911 1.34 217888_s_at ARFGAP1 chr20q13.33 443.7 591.7 0.007846 1.33 204474_at ZNF142 chr2q34-q35 430.9 574.2 0.009064 1.33 32836_at AGPAT1 chr6p21.3 1098.0 1454.7 0.00155 1.32 202774_s_at SFRS8 chr12q24.33 1032.1 1342.7 0.007591 1.30 236254_at VPS13B chr8q22.2 697.5 906.9 0.007215 1.30 226554_at ZBTB7A chr19p13.3 713.8 918.8 0.002756 1.29 228612_at --- --- 1010.7 1290.0 0.001345 1.28 201783_s_at RELA chr11q13 1667.0 2124.1 0.006884 1.27 215004_s_at SF4 chr19p13.11 454.6 571.4 0.006893 1.26 209178_at DHX38 chr16q21-q22.3 573.0 702.6 0.004264 1.23 201511_at AAMP chr2q35 1773.6 1452.0 0.008421 0.82 201768_s_at CLINT1 chr5q23.1-q33.3 1822.3 1455.4 0.008321 0.80 201569_s_at SAMM50 chr22q13.31 2158.0 1712.6 0.008081 0.79 211934_x_at GANAB chr11q12.3 7859.7 6124.3 0.006144 0.78 225088_at C16orf63 chr16p13.11 1459.1 1130.0 0.005534 0.77 217931_at CNPY3 chr6pter-p12.1 900.8 692.5 0.000868 0.77 227072_at RTTN chr18q22.2 1165.0 893.2 0.008913 0.77 218383_at C14orf94 chr14q11.2 1958.6 1492.8 0.005221 0.76 202797_at SACM1L chr3p21.3 3299.8 2439.3 0.00969 0.74 208839_s_at CAND1 chr12q14 1617.3 1189.3 0.004426 0.74 217842_at LUC7L2 chr7q34 1448.0 1061.7 0.003812 0.73 210470_x_at NONO chrxq13.1 9822.3 7097.7 0.002814 0.72 202522_at PITPNB chr22q12.1 6296.2 4511.0 0.009137 0.72 210156_s_at PCMT1 chr6q24-q25 3804.5 2714.7 0.004284 0.71 201994_at MORF4L2 chrxq22 16456.6 11737.6 0.001883 0.71 210779_x_at SIP1 chr14q13 1093.6 776.8 0.003921 0.71 218477_at TMEM14A chr6p12.1 4057.8 2877.2 0.008882 0.71 219350_s_at DIABLO chr12q24.31 3818.0 2685.2 0.006682 0.70 201589_at SMC1A chrxp11.22-p11.21 5881.1 4105.8 0.009271 0.70
202395_at NSF chr17q21 3355.5 2340.9 0.004577 0.70 222697_s_at ABHD10 chr3q13.2 1361.0 939.1 0.009954 0.69 222396_at HN1 chr17q25.1 2979.0 2046.8 0.006068 0.69 239413_at CEP152 chr15q21.1 1582.2 1085.0 0.00796 0.69 221258_s_at KIF18A chr11p14.1 950.5 651.5 0.00251 0.69 204785_x_at IFNAR2 chr21q22.1 21q22.1 1 3998.3 2691.5 0.005739 0.67 219510_at POLQ chr3q13.33 975.4 644.3 0.004528 0.66 202503_s_at KIAA0101 chr15q22.31 23033.4 15170.6 0.004187 0.66 202154_x_at MC1R /// TUBB3 chr16q24.3 4116.1 2689.3 0.00538 0.65 234863_x_at FBXO5 chr6q25-q26 1602.6 1043.2 0.002348 0.65 218719_s_at GINS3 chr16q21 892.9 577.0 0.003274 0.65 209251_x_at TUBA1C chr12q12-q14 32821.5 21167.2 0.002752 0.64 225837_at C12orf32 chr12p13.33 1472.0 940.9 0.001182 0.64 201090_x_at TUBA1B chr12q13.12 35748.6 22805.2 0.008465 0.64 209974_s_at BUB3 chr10q26 13613.5 8621.2 0.0025 0.63 212907_at SLC30A1 chr1q32-q41 3091.6 1954.0 0.008378 0.63 235425_at SGOL2 chr2q33.1 2282.1 1438.8 0.000489 0.63 202338_at TK1 chr17q23.2-q25.3 2497.1 1558.9 0.00522 0.62 201714_at TUBG1 chr17q21 5772.1 3602.1 0.006628 0.62 218248_at FAM111A chr11q12.1 2343.9 1461.2 0.007012 0.62 201897_s_at CKS1B chr1q21.2 20263.5 12540.3 0.003575 0.62 229610_at CKAP2L chr2q13 963.8 595.8 0.006348 0.62 218308_at TACC3 chr4p16.3 2395.8 1480.8 0.004833 0.62 205024_s_at RAD51 chr15q15.1 1842.0 1131.3 0.003725 0.61 212533_at WEE1 chr11p15.3-p15.1 4045.4 2477.2 0.002681 0.61 200973_s_at TSPAN3 chr15q24.3 3926.7 2395.7 0.008638 0.61 228729_at CCNB1 chr5q12 2623.6 1595.4 0.006505 0.61 204444_at KIF11 chr10q24.1 3832.3 2321.7 0.009767 0.61 227687_at HYLS1 chr11q24.2 1955.9 1178.9 0.009643 0.60 209026_x_at TUBB chr6p21.33 32910.2 19793.0 0.002231 0.60 222077_s_at RACGAP1 chr12q13.13 5858.5 3500.6 0.003851 0.60 222439_s_at THRAP3 chr1p34.3 2350.9 1363.8 0.002901 0.58 213007_at FANCI chr15q26.1 3632.7 2106.8 0.008239 0.58 223254_s_at KIAA1333 chr14q12 1421.9 817.2 0.000437 0.57 224753_at CDCA5 chr11q12.1 3445.5 1976.3 0.005246 0.57 210052_s_at TPX2 chr20q11.2 5688.5 3244.7 0.002774 0.57 204162_at NDC80 chr18p11.32 5256.7 2994.4 0.007577 0.57 218039_at NUSAP1 chr15q15.1 11543.5 6535.3 0.004085 0.57 203210_s_at RFC5 chr12q24.2-q24.3 1054.1 596.3 0.006086 0.57 211935_at ARL6IP1 chr16p12-p11.2 14354.0 8099.9 0.002973 0.56 1554768_a_at MAD2L1 chr4q27 7965.3 4468.5 0.00683 0.56 222608_s_at ANLN chr7p15-p14 2012.5 1117.5 0.006846 0.56 228069_at FAM54A chr6q23.3 2280.9 1256.5 0.003822 0.55 203764_at DLG7 chr14q22.3 3846.2 2105.9 0.004367 0.55 213726_x_at TUBB2C chr9q34 14783.5 8079.0 0.002432 0.55 201890_at RRM2 chr2p25-p24 24153.3 12934.7 0.002839 0.54 207165_at HMMR chr5q33.2-qter 11306.7 6037.8 0.00415 0.53
218755_at KIF20A chr5q31 3079.5 1642.9 0.00073 0.53 204826_at CCNF chr16p13.3 1430.7 756.8 0.000195 0.53 211519_s_at KIF2C chr1p34.1 2410.2 1246.4 0.000837 0.52 211762_s_at KPNA2 chr17q24.2 20131.4 10359.1 0.004241 0.51 203418_at CCNA2 chr4q25-q31 3934.3 2009.3 0.004263 0.51 218009_s_at PRC1 chr15q26.1 6888.7 3509.2 0.002328 0.51 217640_x_at C18orf24 chr18q21.1 1655.5 840.4 0.00126 0.51 219990_at E2F8 chr11p15.1 1583.2 771.1 0.005589 0.49 218726_at HJURP chr2q37.1 2998.7 1426.2 0.00024 0.48 209680_s_at KIFC1 chr6p21.3 2390.7 1118.6 0.001231 0.47 204825_at MELK chr9p13.2 6056.8 2831.3 0.003962 0.47 208079_s_at AURKA chr20q13.2-q13.3 6091.1 2840.7 0.001337 0.47 201291_s_at TOP2A chr17q21-q22 10051.2 4548.5 0.000106 0.45 204709_s_at KIF23 chr15q23 1890.2 852.3 0.001754 0.45 225687_at FAM83D chr20q11.22-q12 1944.5 851.0 0.00035 0.44 203214_x_at CDC2 chr10q21.1 4549.4 1582.8 0.000289 0.35
Supplemental Experimental Procedures Microarray data analysis Plasma cell purifications and gene expression profiling, using the Affymetrix HuGene-1_0-st-v1 microarray, were performed as previously described by Zhan et al 2006. Signal intensities were preprocessed and normalized by GCOS1.1 software (Affymetrix). A total of 16 myeloma cell samples (CD138 + and CD138 - ) from 8 myeloma cell lines were used in this study. The Scaling Factor (SF) of each chip was normalized to 500. Affymetrix signals were transformed by the logbase 2 for each sample. The genes defined as drug-resistant related in the analysis were chosen as follows. We compared gene expression profiles from 8 paired myeloma cell lines using a paired t test. A total of 291 probe sets were significantly differentially expressed with p < 0.01 and the average Signal in the higher expression should be > 500) (Supplemental Table 1). Supervised cluster analysis of known classes was performed for Figure 1B using GeneCluster2 (Broad Institute, Cambridge, MA). Cell culture and Sorting ARK, KMS11, ARP1, OCI-MY5 and 5TGM1 et al. cell lines preserved in our lab were cultured in RPMI 1640 containing 2mM L-glutamine, 10% heat-inactivated fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100 μg/ml) in a humidified incubator at 37 C in 5% CO2. Cultures were established by initial suspension at 4X10 5 viable cells/ml and maintained at cell concentrations between 5X10 5 and 1X10 6 viable cells/ml. Medium was changed 2 to 3 times per week. We used automacs and CD138 microbeads (Miltenyi Biotec Inc., Auburn, CA) for sorting since automacs system has lower pressure and shorter time period than flow cytometry sorter. To avoid non-viable cells after sorting by our experience, following points are critical. A) Total amount of cells should be more than 20M with viability above 95% before sorting. B) CD138-
microbeads incubation for only 20mins at 4 degree Celsius, gently shake incubation tube every 5 minutes. C) Using depletion protocol for automacs separator. D) Add 5ml of RPMI 1640 with 10% FBS and 1% PSG to collecting tube for CD138 +/- cells. After sorting, cell viability was checked again by trypan blue to confirm that the viability was around 90% for the following cell growth and Real time PCR study.