Supplemental Data: Table S2 tracking_id A375P SK-MEL2 Fold change des ZEB2-AS1 1.35E-286 0.315166 2.3284E+285 ZEB2 antisense RNA 1 PCDHGC5 5.45E-242 0.284138 5.2132E+240 protocadherin gamma subfamily C, 5 APOBEC3B-AS1 3.98E-240 0.130813 3.2873E+238 APOBEC3B antisense RNA 1 C6orf201 1.14E-227 0.15186 1.3345E+226 chromosome 6 open reading frame 201 LRRC24 1.93E-168 0.459062 2.3783E+167 leucine rich repeat containing 24 ZACN 3.22E-158 0.0670639 2.0857E+156 zinc activated ligand-gated ion channel LOC100506071 1.62E-144 3.33E-38 2.0564E+106 uncharacterized LOC100506071 EGFR-AS1 4.29E-101 0.0771076 1.7966E+99 EGFR antisense RNA 1 PRR5-ARHGAP8 3.44E-103 3.89E-10 1.13143E+93 PRR5-ARHGAP8 readthrough LOC100129148 8.77E-284 2.60E-214 2.96023E+69 uncharacterized LOC100129148 VLDLR-AS1 3.00E-65 0.0959249 3.20259E+63 VLDLR antisense RNA 1 ZASP 4.04E-72 4.00E-16 9.91857E+55 ZO-2 associated speckle protein SYNE1-AS1 7.86E-57 0.166307 2.11625E+55 SYNE1 antisense RNA 1 MED4-AS1 8.51E-47 0.193771 2.27656E+45 MED4 antisense RNA 1 MSTO2P 2.80E-42 0.111398 3.97942E+40 misato family member 2, pseudogene CABP7 2.99E-36 0.0263724 8.82596E+33 calcium binding protein 7 KCTD14 1.36E-151 3.05E-121 2.23303E+30 potassium channel tetramerization domain containing 14 RAET1E-AS1 1.26E-31 0.215175 1.71406E+30 RAET1E antisense RNA 1 ST7-OT3 2.06E-30 0.0817968 3.98019E+28 ST7 overlapping transcript 3 PKLR 3.86E-28 0.0268357 6.9509E+25 pyruvate kinase, liver and RBC LY75-CD302 2.64E-26 0.184984 7.01824E+24 LY75-CD302 readthrough TMEM189-UBE2V1 7.87E-23 0.322541 4.09933E+21 TMEM189-UBE2V1 readthrough PGBD3 2.12E-28 4.44E-07 2.0928E+21 piggyBac transposable element derived 3 XAGE1E 3.68E-18 0.122103 3.32106E+16 X antigen family, member 1E HSPE1-MOB4 2.23E-17 0.157601 7.06262E+15 HSPE1-MOB4 readthrough FIGF 2.43E-16 0.429744 1.77085E+15 c-fos induced growth factor (vascular endothelial growth factor D) TBC1D3 2.47E-42 1.02E-29 4.12291E+12 TBC1 domain family, member 3 CT45A1 8.67E-18 9.94E-07 1.14715E+11 cancer/testis antigen family 45, member A1 MRPL42P5 1.23E-12 0.138235 1.12105E+11 mitochondrial ribosomal protein L42 pseudogene 5 ADORA2A 1.89E-25 1.69E-15 8945107222 adenosine A2a receptor LOC100133286 7.26E-11 0.0851365 1171951033 uncharacterized LOC100133286 KLF3-AS1 1.67E-09 0.253589 151799706.7 KLF3 antisense RNA 1 TP53TG3 1.10E-09 0.162432 147676194.6 LOC101927051 4.03E-10 0.0397308 98679661.42 uncharacterized LOC101927051 LOC100288866 8.54E-09 0.594396 69611023.54 uncharacterized LOC100288866 RNF157-AS1 3.09E-09 0.0342455 11088032.74 RNF157 antisense RNA 1 TP53TG3B 1.41E-12 8.99E-06 6360086.599 TP53 target 3B LOC285819 1.06E-83 2.13E-77 2002227.465 uncharacterized LOC285819 DPY19L2P3 1.94E-07 0.169621 875779.6365 DPY19L2 pseudogene 3 SAA2-SAA4 1.95E-07 0.134017 686355.0464 SAA2-SAA4 readthrough LOC103171574 3.03E-07 0.179603 591876.0113 uncharacterized LOC103171574 SAPCD1 1.93E-06 0.661436 343177.0425 suppressor APC domain containing 1 SPTY2D1-AS1 2.72E-07 0.0929461 342060.6939 SPTY2D1 antisense RNA 1 RGPD2 1.40E-07 0.02554 182007.3544 RANBP2-like and GRIP domain containing 2 TNNI3K 3.08E-12 1.28E-07 41393.05032 TNNI3 interacting kinase SYNJ2BP-COX16 3.52E-06 0.0966859 27471.33132 SYNJ2BP-COX16 readthrough MMP23B 2.47E-06 0.0638591 25906.11841 matrix metallopeptidase 23B RNF103-CHMP3 5.15E-06 0.129952 25241.68125 RNF103-CHMP3 readthrough DNAJC25-GNG10 1.58E-05 0.312706 19831.05559 DNAJC25-GNG10 readthrough BOLA2B 1.43E-05 0.243764 17079.75701 bolA family member 2B URGCP-MRPS24 1.10E-07 0.00121781 11090.45871 URGCP-MRPS24 readthrough H3F3A 0.00141218 6.86913 4864.202864 H3 histone, family 3A DCT 0.0624829 284.921 4559.983612 dopachrome tautomerase LOC541473 2.32E-05 0.081158 3505.487718 FK506 binding protein 6, 36kDa pseudogene ZNF625-ZNF20 0.000123639 0.329237 2662.889541 ZNF625-ZNF20 readthrough (NMD candidate) PMEL 0.426334 1072.75 2516.219678 premelanosome protein RPS4Y1 0.0919449 180.389 1961.925022 ribosomal protein S4, Y-linked 1 MAGEA10-MAGEA5 2.31E-05 0.0400526 1731.622431 RGPD6 2.50E-05 0.0226537 904.3682034 RANBP2-like and GRIP domain containing 6 CELF2 0.0168651 15.1924 900.8188508 CUGBP, Elav-like family member 2 MYEOV 0.188445 162.359 861.5723421 myeloma overexpressed LCP1 0.183462 134.08 730.832543 lymphocyte cytosolic protein 1 (L-plastin) TMC5 0.0188893 13.4806 713.6632909 transmembrane channel-like 5 ARMCX1 0.0338789 23.3065 687.9355587 armadillo repeat containing, X-linked 1 ITIH5 0.173853 113.085 650.4633225 inter-alpha-trypsin inhibitor heavy chain family, member 5 LINC00518 0.0233296 13.8745 594.7165832 long intergenic non-protein coding RNA 518 SSX1 0.118177 68.7288 581.575095 synovial sarcoma, X breakpoint 1 ALDH1L1 0.0235821 12.9787 550.3623511 aldehyde dehydrogenase 1 family, member L1 PHKA2-AS1 0.0620347 33.9326 546.9938599 PHKA2 antisense RNA 1 LOC146481 0.080657 42.666 528.9807456 SMIM10 0.0487491 23.9358 490.9998338 small integral membrane protein 10 CAPN3 0.504442 219.645 435.4217135 calpain 3, (p94) LOC100507065 0.0974265 40.9329 420.1413373 uncharacterized LOC100507065 KCNN2 0.103505 43.4419 419.7082267 potassium channel, calcium activated intermediate/small conductance subfamily N alpha, member 2 GALM 0.0287394 11.9635 416.275218 galactose mutarotase (aldose 1-epimerase) BIRC7 0.0582455 23.5514 404.3471169 baculoviral IAP repeat containing 7 TBC1D3C 6.66E-10 2.53E-07 379.5507207 TBC1 domain family, member 3C BMX 0.169632 63.9133 376.7761979 BMX non-receptor tyrosine kinase SLC24A5 0.055791 20.6956 370.9487193 solute carrier family 24 (sodium/potassium/calcium exchanger), member 5 PCNA-AS1 2.65E-07 9.56E-05 360.5274772 PCNA antisense RNA 1 INO80B-WBP1 0.00457204 1.62935 356.3726477 INO80B-WBP1 readthrough (NMD candidate) SLC15A1 0.0224679 7.7178 343.5033982 solute carrier family 15 (oligopeptide transporter), member 1 MLANA 0.49183 168.94 343.4926702 melan-A RFPL4B 0.0384573 12.222 317.8070223 ret finger protein-like 4B LOC101927040 0.0341406 10.7807 315.7735951 uncharacterized LOC101927040 GPR128 0.0223693 6.92704 309.6672672 STXBP2 0.155013 42.6336 275.0324166 syntaxin binding protein 2 MEIOB 0.0430797 11.6798 271.1207367 meiosis specific with OB domains TSPAN7 0.0406748 10.9249 268.5913637 tetraspanin 7 LOC400644 0.0391152 10.2656 262.4452898 RGS1 0.0540326 14.0118 259.3212246 regulator of G-protein signaling 1 CNDP1 0.0655798 16.7417 255.2874513 carnosine dipeptidase 1 (metallopeptidase M20 family) GPM6B 0.109051 26.7367 245.1761103 glycoprotein M6B MB21D1 0.0407749 9.99031 245.0112692 Mab-21 domain containing 1 TRIM48 0.104489 25.5973 244.9760262 tripartite motif containing 48 ATP6V0D2 0.151097 36.9015 244.2239091 ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2 STK32A 0.0279351 6.67584 238.9767712 serine/threonine kinase 32A FLJ16779 0.00888566 2.08682 234.8525602 uncharacterized LOC100192386 ALDH3B2 0.0572018 13.373 233.7863494 aldehyde dehydrogenase 3 family, member B2 FILIP1 0.0294972 6.77665 229.7387549 filamin A interacting protein 1 PRUNE2 0.01603 3.39768 211.9575795 prune homolog 2 (Drosophila) CLDN14 0.0420915 8.89957 211.4339 claudin 14 CHL1 0.034005 7.09565 208.6649022 cell adhesion molecule L1-like OCIAD2 0.260965 53.1906 203.8227348 OCIA domain containing 2 APOD 1.8068 368.038 203.6960372 apolipoprotein D LOC100128682 0.0211425 4.16248 196.8773797 FAM167B 1.44485 262.289 181.5337232 family with sequence similarity 167, member B SCN9A 0.0207549 3.76748 181.5224357 sodium channel, voltage gated, type IX alpha subunit MAGEA1 0.345986 62.0685 179.3959871 melanoma antigen family A1 PHACTR1 0.13181 22.6246 171.6455504 phosphatase and actin regulator 1 DPPA4 0.025105 4.09289 163.0308703 developmental pluripotency associated 4 SCARNA13 4.74E-06 0.00075542 159.2668102 small Cajal body-specific RNA 13 MYCN 0.054592 8.50811 155.8490255 v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog ECHDC3 0.0448575 6.89751 153.7649223 enoyl CoA hydratase domain containing 3 CA8 0.15771 23.7692 150.7146028 carbonic anhydrase VIII MATN2 0.0505877 7.45796 147.4263507 matrilin 2 LDB3 0.0415073 5.76998 139.0112101 LIM domain binding 3 DNAH6 0.0367808 5.03326 136.8447668 dynein, axonemal, heavy chain 6 PROM1 0.0179822 2.3955 133.2150682 prominin 1 XKR8 0.0669032 8.29965 124.0546043 XK, Kell blood group complex subunit-related family, member 8 CPED1 0.249591 30.8613 123.6474873 cadherin-like and PC-esterase domain containing 1 TMX2-CTNND1 6.16E-06 0.000758202 123.1087225 TMX2-CTNND1 readthrough (NMD candidate) FUT4 0.0225832 2.54757 112.8081937 fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific) ADAMTS2 0.0403372 4.46274 110.6358399 ADAM metallopeptidase with thrombospondin type 1 motif, 2 WNK3 0.0120559 1.30982 108.6455594 WNK lysine deficient protein kinase 3 TMEM232 0.0219837 2.3669 107.6661345 transmembrane protein 232 LOC100133445 0.282585 30.1585 106.7236407 TLR2 0.0205527 2.17072 105.6172668 toll-like receptor 2 CA14 0.042364 4.47316 105.5887074 carbonic anhydrase XIV LINC00634 0.0498486 5.26295 105.5786923 long intergenic non-protein coding RNA 634 TDRP 0.0204198 2.13342 104.4780066 testis development related protein NSG1 0.17743 18.4474 103.9700163 neuron specific gene family member 1 SLC24A2 0.00623271 0.639807 102.6530995 solute carrier family 24 (sodium/potassium/calcium exchanger), member 2 P2RX7 0.0603769 5.91636 97.99045662 purinergic receptor P2X, ligand gated ion channel, 7 LOC157273 0.020301 1.9776 97.4139205 uncharacterized LOC157273 FAT2 0.0369389 3.5896 97.17668907 FAT atypical cadherin 2 TPTEP1 0.105739 10.1879 96.34950208 transmembrane phosphatase with tensin