Figure S1. RNA degradation map of the three gene chips. Each of the 76 samples is presented by a differently colored line. Table SI. Upregulated (n=1,300) and downregulated (n=912) differentially expressed genes. A, Upregulated genes Gene Log fold Average t P-value Adjusted change expression P-value LINGO1 2.6777 6.4170 23.1699 5.54x10-37 1.69x10-33 VWF 1.6093 6.2905 23.0801 7.24x10-37 1.74x10-33 PYCR1 1.4290 7.4945 22.2201 9.80x10-36 1.93x10-32 DTL 2.7697 6.1038 21.9223 2.46x10-35 4.09x10-32 CKAP2L 1.9408 6.7911 21.8106 3.48x10-35 5.31x10-32 CASC5 1.0329 4.9592 21.7923 3.68x10-35 5.31x10-32 RDM1 1.8612 5.8981 21.4909 9.46x10-35 1.28x10-31 HMGA1 1.9524 7.0245 21.2584 1.97x10-34 2.37x10-31 GRHL2 2.3061 6.6285 21.2028 2.35x10-34 2.68x10-31 EMC3-AS1 1.7596 6.4341 20.7583 9.76x10-34 1.06x10-30 DSN1 1.5764 5.6077 20.7126 1.13x10-33 1.16x10-30 CENPF 2.0079 6.1039 20.5981 1.64x10-33 1.48x10-30 BIK 2.8614 6.9592 20.4699 2.48x10-33 2.15x10-30 CDCA8 1.8125 7.2037 20.3946 3.18x10-33 2.45x10-30 CCNB2 1.3002 6.2043 19.9845 1.22x10-32 8.81x10-30 DUSP9 1.7127 6.3549 19.8314 2.03x10-32 1.42x10-29 ESPL1 2.0699 7.4012 19.4946 6.27x10-32 4.11x10-29 CSPG5 2.0283 6.6777 19.3062 1.18x10-31 7.32x10-29 CDCA5 2.5265 7.5517 19.1695 1.88x10-31 1.10x10-28 KIF20B 2.2678 6.4109 19.0425 2.90x10-31 1.57x10-28 E2F1 1.4217 7.0710 19.0116 3.23x10-31 1.70x10-28 CDCA3 2.2727 7.4162 18.9327 4.23x10-31 1.99x10-28 MUC1 2.2947 7.7898 18.8818 5.04x10-31 2.27x10-28 KIF2C 1.6191 7.1943 18.7275 8.57x10-31 3.71x10-28 BIRC5 1.6937 6.5189 18.7158 8.92x10-31 3.78x10-28 CLPB 1.3245 6.0626 18.6137 1.27x10-30 5.06x10-28 EP400NL 1.1052 5.7688 18.5549 1.56x10-30 6.02x10-28 EME1 1.2678 7.1363 18.4322 2.39x10-30 8.91x10-28 CDC25A 1.1725 5.7785 18.3774 2.89x10-30 1.06x10-27 PCDH19 2.8519 6.7964 18.2888 3.94x10-30 1.42x10-27 AURKA 1.9448 7.1259 18.0847 8.09x10-30 2.82x10-27 AUNIP 1.5254 6.3633 18.0666 8.62x10-30 2.91x10-27 RP11-932O 1.3832 5.1724 18.0047 1.07x10-29 3.46x10-27 MCM4 1.1376 6.2140 17.9771 1.18x10-29 3.76x10-27 LZTS3 1.8255 8.3889 17.8586 1.80x10-29 5.41x10-27 NCAPG 2.6668 6.4147 17.8481 1.87x10-29 5.54x10-27 CENPN 1.4763 5.7550 17.7921 2.28x10-29 6.67x10-27 KLHL14 1.9600 5.9395 17.7846 2.34x10-29 6.76x10-27 PLK4 1.1343 5.0519 17.7476 2.68x10-29 7.53x10-27 MKI67 1.8325 6.3716 17.7471 2.68x10-29 7.53x10-27 NEK2 1.7269 5.8034 17.6770 3.44x10-29 9.43x10-27 PTTG3P 2.1969 5.8490 17.6113 4.36x10-29 1.16x10-26 KIF14 2.2546 5.5588 17.5651 5.15x10-29 1.36x10-26 SPC24 1.4253 6.8535 17.5565 5.31x10-29 1.38x10-26 ERCC6L 2.1262 5.9470 17.2792 1.45x10-28 3.55x10-26 SLC52A2 1.5393 6.9230 17.2709 1.49x10-28 3.62x10-26 HIST1H2AJ 1.6594 6.7777 17.2660 1.52x10-28 3.64x10-26 MICALL2 1.3003 5.9194 17.2489 1.61x10-28 3.75x10-26 LRP8 2.0300 6.3153 17.2223 1.78x10-28 4.04x10-26 C12orf56 2.3795 6.0955 17.1358 2.43x10-28 5.48x10-26 SAPCD2 1.4331 7.3571 17.1303 2.48x10-28 5.54x10-26 PAX8 1.3725 6.7447 17.0753 3.04x10-28 6.70x10-26 UHRF1 2.5390 6.8479 17.0605 3.20x10-28 7.00x10-26 SPC25 2.8074 5.5202 16.9703 4.46x10-28 9.27x10-26 CCDC88C 1.1785 5.7025 16.9567 4.69x10-28 9.65x10-26 OVOL2 1.4644 6.3946 16.8572 6.75x10-28 1.34x10-25 NBPF4 1.7451 5.5536 16.8483 6.98x10-28 1.37x10-25 RECQL4 1.2008 6.8084 16.8017 8.29x10-28 1.61x10-25 CLDN4 1.5144 6.9890 16.7947 8.50x10-28 1.64x10-25 FAM90A1 1.5786 6.1458 16.7882 8.71x10-28 1.67x10-25 KIR3DL1 1.4547 6.0756 16.7322 1.07x10-27 2.01x10-25 BSPRY 1.3826 6.3805 16.7127 1.15x10-27 2.15x10-25 LOC100507 1.3755 5.0280 16.7019 1.20x10-27 2.22x10-25 LINC00858 1.5576 5.6509 16.6854 1.27x10-27 2.31x10-25 PSAT1 2.5168 7.3518 16.6618 1.39x10-27 2.50x10-25 GLDC 3.1429 7.0894 16.5717 1.94x10-27 3.44x10-25 KIF4A 2.2143 7.2671 16.5696 1.96x10-27 3.44x10-25 CCNE1 1.7901 6.7954 16.4809 2.72x10-27 4.71x10-25 LOC100289 1.8220 6.5782 16.4481 3.08x10-27 5.24x10-25 NUSAP1 2.2603 7.8854 16.4116 3.53x10-27 5.87x10-25 FKBP4 1.1954 6.2994 16.3485 4.46x10-27 7.29x10-25 KLHL23 1.1779 5.2137 16.3134 5.09x10-27 8.22x10-25 BDH1 1.4746 6.3460 16.2895 5.57x10-27 8.92x10-25 WFDC2 1.7254 6.6776 16.2783 5.81x10-27 9.24x10-25 DBN1 1.4444 7.3256 16.2659 6.09x10-27 9.61x10-25 SOX17 3.8416 7.7496 16.2443 6.60x10-27 1.03x10-24 RASAL1 1.4102 6.3427 16.2235 7.14x10-27 1.10x10-24 FAM64A 2.3019 6.5414 16.2177 7.29x10-27 1.12x10-24 STC2 2.0560 6.2749 16.1653 8.88x10-27 1.35x10-24 WSCD2 1.2448 6.3078 16.1410 9.74x10-27 1.47x10-24 CDC20 2.0685 7.3723 16.1211 1.05x10-26 1.57x10-24 RP11-108L 1.7928 5.3868 16.1145 1.08x10-26 1.59x10-24 KIF20A 2.4329 6.3827 16.0906 1.18x10-26 1.73x10-24 GCAT 1.2301 6.9910 16.0277 1.49x10-26 2.18x10-24 CBX2 1.1590 6.4876 15.9948 1.69x10-26 2.46x10-24 PARPBP 1.3242 5.2212 15.9852 1.75x10-26 2.53x10-24 MCM5 1.7791 6.8659 15.9754 1.82x10-26 2.61x10-24 LOC100130 1.8653 5.3499 15.9672 1.88x10-26 2.67x10-24 CENPL 1.2460 6.1142 15.8533 2.90x10-26 4.04x10-24 AKT1 1.5287 6.7459 15.8325 3.13x10-26 4.32x10-24 HAGLROS 1.7122 6.3663 15.8022 3.52x10-26 4.79x10-24 CAPN5 1.2231 5.9417 15.7908 3.68x10-26 4.97x10-24 MCM10 2.0964 5.6301 15.7722 3.95x10-26 5.30x10-24 DNMT3B 1.9281 7.4579 15.7335 4.58x10-26 6.11x10-24 C1orf210 1.3742 6.0029 15.7092 5.02x10-26 6.66x10-24 BC047644 1.0095 5.5583 15.7058 5.09x10-26 6.71x10-24 CLEC4F 1.1497 5.8508 15.6568 6.13x10-26 7.92x10-24 RAD51 1.1495 5.9131 15.6561 6.15x10-26 7.92x10-24 LOC100506 1.8291 5.5014 15.6498 6.30x10-26 8.07x10-24 WBSCR27 1.2391 5.9734 15.6466 6.38x10-26 8.12x10-24 KIF23 2.1667 5.1610 15.5031 1.11x10-25 1.37x10-23 DLG3-AS1 1.3617 5.9570 15.4810 1.21x10-25 1.48x10-23 HIST1H4J 1.6780 7.0089 15.4750 1.23x10-25 1.51x10-23 LOC101928 1.1079 5.4239 15.4452 1.38x10-25 1.66x10-23 RP11-456H 1.0877 5.7331 15.3471 2.02x10-25 2.35x10-23 SYTL1 1.7593 6.3074 15.3405 2.08x10-25 2.40x10-23 CTA-250D1 1.0507 5.9567 15.3351 2.12x10-25 2.44x10-23 CD300C 1.3871 6.1556 15.3306 2.16x10-25 2.46x10-23 PSRC1 2.2015 7.1633 15.3111 2.33x10-25 2.62x10-23 TIGIT 1.3562 5.5120 15.3019 2.41x10-25 2.69x10-23 KATNAL2 1.0753 5.5831 15.2954 2.47x10-25 2.74x10-23 PRSS2 2.0386 6.4592 15.2903 2.52x10-25 2.78x10-23 CBS 1.3384 6.7482 15.2528 2.92x10-25 3.17x10-23 GNGT1 1.8856 5.2198 15.2503 2.94x10-25 3.18x10-23 TMPRSS4 2.1574 7.2496 15.2382 3.09x10-25 3.32x10-23 LOC101927 1.2973 5.0137 15.2208 3.30x10-25 3.48x10-23 SIPA1 1.1424 6.1818 15.1822 3.84x10-25 3.99x10-23 SOX9 2.4172 6.9251 15.1379 4.56x10-25 4.72x10-23 RAD54L 1.5487 6.8337 15.1125 5.03x10-25 5.16x10-23 GIPC1 1.2689 7.7226 15.0835 5.64x10-25 5.73x10-23 FAM174B 1.5871 7.0617 15.0497 6.43x10-25 6.47x10-23 RP1-74M1.