100bp CST6 TAC1

BGS BGS -228 +194 -441 -166

LN229 LN229

TACSTD2 BIK

BGS BGS -415 -168 -765 -596

LN229 LN229

CDO1 CLIC3

BGS BGS -504 -252 -203 -35

LN229 LN229

Kim et al., Online Supplementary Figure 1 100bp TSPYL5

BGS -353 +130

LN229

Kim et al., Online Supplementary Figure 1 cont. RNASET2 TFDP3

MSP (-677 to -503) MSP (-146 to -28) BGS BGS -380 -45 -146 -28

T98G T98G

Normal Normal brain brain CDA*

MSP (-99 to +10) BGS

-104 +43

T98G

Normal brain

*not a CpG island

Kim et al., Online Supplementary Figure 2 TSPYL5 BGS in Primary Brain Tumors

100bp TSPYL5

BGS MSP -353 (-29 to +77) +130

T9

T29

T34

Kim et al., Online Supplementary Figure 3 Online Supplementary Table 1 - Kim et al. Primer sequences for RT-PCR analysis of all described in this paper.

Gene name Primer Sequence (5'-3') C1orf34 forward aaggggctgtgggatttagt reverse gggcttgaggtagctgagtg TACSTD2 forward gatttcggtatcgtcccaga reverse ggaccgaaaggggatacatt TSPAN1 forward tcctgacgttgctggtagtg reverse gctgtgttggtgacgttgtc SFN forward ggatcccactcttcttgcag reverse ctgccactgtccagttctca CDA forward ctgaagcctgagtgtgtcca reverse tgagacggccttctggatag FBXO2 forward tccatagcgtcctcaccttc reverse cactttgtggcaagcactgt S100A2 forward atgagtgggaatggcaagag reverse ctgctccagagaactgcaca ATF3 forward gccattggagagctgtcttc reverse gggccatctggaacataaga BIA2 forward tctggtcttcttcggcctta reverse tatccttcaccccactccag FLJ22595 forward caaaccaaacaagcccaagt reverse cagccccaaacagttctcat DKFZP434N1235 forward gtgagcctgcgaaaaagaag reverse gtccaccatgcctttgtacc KIAA0888 forward accagcgaataccagtcac reverse agtgcttgcaaaggcatctt CDO1 forward acctgctgtgagccttcact reverse ggcaaacatacagcgaacct FAM50B forward caccatggagaaggacgagt reverse tgatggggcctagaaatgag RNASET2 forward gaagcatgagtgggaaaagc reverse tactctggcaagggcatctt TAC1 forward tcgcaaaatccaacatgaaa reverse aaagaactgctgaggcttgg LRCH4 forward gctgtgtcacccctcattct reverse ttggacaggtacaggggaac TES forward tgtgtcaaggatgccacaat reverse gccctcctcctaagacatcc CLU forward gtcaacggggtgaaacagat reverse tcaggcagggcttacactct TSPYL5 forward tgggaacagcgggaaccgt reverse ctgcatccctctcttccttc ADFP forward ccgtcgatttctttctccag reverse tgatggtcttcacaccgttc C9orf3 forward cttctgaggccaacttcagg reverse tgctcccagaacagaatgtg CLIC3 forward agctgtttgtcaaggcgagt reverse cgctgtcatagagcaggatg Hrasls3 forward acaaggccatcgtgaagaag reverse actccatagcgcagctcatt CST6 forward ctacttccgagacacgcaca reverse ggaaccacaaggacctcaaa NINJ2 forward ccctcatcagcctctctctg reverse cagccaggaaccctgtttta FGD6 forward ttgtatgccaagcttgttcg reverse ttctgtttcctccctgatgg GCHFR forward ggtgtctgcacaaggagtga reverse gacgcagggtttcagagaag RPP25 forward cgtgcgataattgctgctta reverse tctgaagcaggggaaagaaa SMPD3 forward gagggctgcatctctaccag reverse ccagactctgttgtgcctga SERPINF1 forward ttgagaagaagctgcgcata reverse accgagaaggagaatgctga ARHN forward tgggacacttcaggttcctc reverse cagtccgcatgtccagttta TGM2 forward gccataggcccaggatattt reverse cagctaaggctgttgggaag WISP2 forward ctccctgcctacacacacag reverse aaactccagaaaaggcagca C20orf35 forward tgtcgggagaagaccagact reverse ggcatcttgtccaacctcat BIK forward tgaagaggacctggacccta reverse ccctgatgtcctcagtctgg NXT2 forward cgacactgccagaacacact reverse ccctgaaacagcatttccat TFDP3 forward tcagggaacttttggaggtg reverse tctcactgaggtcgtcatcg TSPYL1 forward tgaccaagtcccgagcgacc reverse ggccttcggcgggaggctgg TSPYL3 forward ccacggcgactactccgagc reverse tcccactggatggcctccag TSPYL4 forward cctggctgctcccgaccatg reverse ccacggggctctccaagctg TSPYL6 forward cttgggcaacagcattaggt reverse cattcgcttcgcttagaagg β- forward aaaagccaccccacttctct reverse ctcaagttgggggacaaaaa Online Supplementary Table 2 - Kim et al. Primer sequences for methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS) used in this study. TACSTD2 MSP Primer Sequence (5'-3') M F TATATTTTATTCGATTTGTTCGG R AACCGACTTAACCTTCCGTA

U F TTTTATATTTTATTTGATTTGTTTGG R CAAAACCAACTTAACCTTCCATA BGS F TTATTGGTATTTGGGTGATATATTT R ACAATAAAACTCTTTAAACTTTCTACC

CDA MSP M F ATATTTAAGGGGAGGAGTTGTAATC R TTCTAAACCATATTAATACCCCGAA

U F TATTTAAGGGGAGGAGTTGTAATTGT R TTCTAAACCATATTAATACCCCAAA BGS F AGTGTGTTTATTAGTGAGAGTGG R ACACACTCAAACTTCAAAATACAAAC

CDO1 MSP M F TTAGATTTGTGGGGTTTATTTTTTC R CCACCTTTCTTAAATAACTCTCCG

U F TAGATTTGTGGGGTTTATTTTTTTG R CACCTTTCTTAAATAACTCTCCACC BGS F GTTAAAGTGGGGGAGAGATTG R TTCAAATCTATAAAATTCATCCTC

RNASET2 MSP M F AGAGGTCGAGGTAGGAGTAGTTTC R CCCACTTACTAACGAAAAATAACG

U F GAGAGGTTGAGGTAGGAGTAGTTTT R CCACTTACTAACAAAAAATAACACA BGS F GTTTTGGGTTGGGAGTAA R CCCACTTCCCACCTACTACC

TAC1 MSP M F TTAGATTTGTAGACGGAAGTAGGTC R GTAATTAAAAATTTCCGAAACGAT

U F AGATTTGTAGATGGAAGTAGGTTGT R CATAATTAAAAATTTCCAAAACAAT BGS F GGTTTAAGGAGGTTGGGATAAATAT R TTAAAAAACCAATCTCCCCACTAT

TSPYL5 MSP M F GTGTTTTTGAAGTTGTTTTCGTC R CGAACTCGAACTTTAACGCG

U F TGTGTTTTTGAAGTTGTTTTTGTT R AAAACAAACTCAAACTTTAACACA BGS F ATAGGTGGTGATGGTTTTTAG R AAACTCTAATACTATAAAAAATC

CLIC3 MSP M F TTTTTTAAGTTTTTTTGTGCGTTTC R TTACTCAAACAACTAATTCTACGCG

U F TTTTAAGTTTTTTTGTGTGTTTTGT R ACTCAAACAACTAATTCTACACACT BGS F TTTGGGGAGTTTTTTAAGTTTTTTT R CTAAAATCACACCCTCAAACTCAA

CST6 MSP M F GATTTGTCGTTCGACGATTC R CGACCACCAACTAACTCTACG

U F GGGATTTGTTGTTTGATGATTT R TACCAACCACCAACTAACTCTACAC BGS F GGTGTGTTTTGGAGGGTAGGGAAG R CTATTACTACCCATATTATAACTAACC BIK MSP M F GTTTTTTGATTTTTTTGTTCGTTTC R AAACTACCCCTCCACTACCG

U F TTTTTGATTTTTTTGTTTGTTTTGT R AACTACCCCTCCACTACCAC BGS F GTTTGGAAGTTTTTTGATTTTTTTG R TCCAACTACATAACACACCCACTAC

TFDP3 MSP M F GATATTGGATTGTTTAAAGGTTTTC R ATATCAATCTCACTAAAACTAACGAA

U F ATTGGATTGTTTAAAGGTTTTTGG R TATCAATCTCACTAAAACTAACAAA BGS F GATATTGGATTGTTTAAAGGTTTT R CAAAATATATCAATCTCACTAAAACTAAC Online Supplementary Table 3 - Kim et al. Genes up- and down-regulated in 3 out of 4 glioma cell lines after treatment with 5-azadC and TSA by SAM analysis (FDR

160 Positive Significant Genes (Up-regulated Genes)

Gene ID Gene Title Ave. Fold Change 205700_at 3-hydroxysteroid epimerase 4.51723 206588_at deleted in azoospermia-like 11.70766 218966_at 5C 2.44777 207180_s_at HIV-1 Tat interactive 2, 30kDa 3.79867 206218_at melanoma antigen, family B, 2 9.30517 210652_s_at 1 open reading frame 34 5.18257 219928_s_at calcium-binding tyrosine-(Y)-phosphorylation regulated (fibrousheathin 2) 2.83923 205627_at cytidine deaminase 22.97368 205775_at DNA segment on chromosome 6(unique) 2654 expressed sequence 3.78819 215881_x_at synovial sarcoma, X breakpoint 3 2.97778 218094_s_at chromosome 20 open reading frame 35 2.84382 219529_at chloride intracellular channel 3 12.93814 203571_s_at adipose specific 2 27.17740 203786_s_at tumor protein D52-like 1 4.66233 209628_at hypothetical protein P15-2 3.02915 202286_s_at tumor-associated calcium signal transducer 2 9.94012 202719_s_at testis derived transcript (3 LIM domains) 7.48516 210233_at interleukin 1 receptor accessory protein 2.11739 221577_x_at prostate differentiation factor 5.75178 202704_at transducer of ERBB2, 1 2.00639 204268_at S100 calcium binding protein A2 7.21552 208792_s_at clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone 2.62200 217755_at hematological and neurological expressed 1 2.03761 209122_at adipose differentiation-related protein 6.86038 209270_at laminin, beta 3 3.30863 212848_s_at chromosome 9 open reading frame 3 2.20694 210437_at melanoma antigen, family A, 9 5.37259 201650_at 19 44.71695 33322_i_at stratifin 9.56412 209260_at stratifin 15.92832 210619_s_at hyaluronoglucosaminidase 1 5.33884 216471_x_at synovial sarcoma, X breakpoint 2 8.79754 204134_at phosphodiesterase 2A, cGMP-stimulated 4.88273 208981_at platelet/endothelial cell adhesion molecule (CD31 antigen) 3.36022 220057_at G antigen, family D, 2 5.52070 218451_at hypothetical protein FLJ22969 3.29663 203917_at coxsackie virus and adenovirus receptor 4.89969 221805_at , light polypeptide 68kDa 3.90021 209448_at HIV-1 Tat interactive protein 2, 30kDa 5.94066 211670_x_at 4.91805 214262_at complement component 1, q subcomponent binding protein 3.23270 33304_at interferon stimulated gene 20kDa 2.17032 203951_at calponin 1, basic, smooth muscle 5.29412 203407_at 3.96497 213467_at ras homolog gene family, member N 3.23985 210253_at HIV-1 Tat interactive protein 2, 30kDa 3.39439 206595_at cystatin E/M 3.49210 211003_x_at transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) 3.22455 211731_x_at synovial sarcoma, X breakpoint 3 3.49418 219695_at hypothetical protein FLJ22593 3.17405 215734_at hypothetical protein IMAGE:4215339 6.63789 202957_at hematopoietic cell-specific Lyn substrate 1 2.21941 219305_x_at F-box only protein 2 4.15068 217984_at ribonuclease 6 precursor 2.11442 202411_at interferon, alpha-inducible protein 27 5.47341 206626_x_at synovial sarcoma, X breakpoint 1 5.19851 205245_at par-6 partitioning defective 6 homolog alpha (C.elegans) 2.05304 213620_s_at intercellular adhesion molecule 2 6.30709 202283_at serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithe 21.25825 210130_s_at transmembrane 7 superfamily member 2 2.25644 205780_at BCL2-interacting killer (apoptosis-inducing) 6.28840 219045_at ras homolog gene family, member F (in filopodia) 3.13501 219143_s_at hypothetical protein FLJ20374 4.25421 216462_at synovial sarcoma, X breakpoint 2 3.01995 208791_at clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone 2.43340 219901_at hypothetical protein FLJ11183 3.23623 204867_at GTP cyclohydrolase I feedback regulatory protein 3.15974 206552_s_at tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuro 7.14508 213506_at coagulation factor II (thrombin) receptor-like 1 6.41143 206093_x_at tenascin XB 3.49461 218963_s_at type I 8.88377 201212_at legumain 2.83349 220468_at hypothetical protein FLJ22595 6.08153 209114_at tetraspan 1 6.59637 210854_x_at solute carrier family 6 (neurotransmitter transporter, creatine), member 8 2.16260 206897_at G antigen, family B, 1 (prostate associated) 2.05315 214412_at H2A histone family, member B 13.90675 218729_at latexin protein 9.31484 211425_x_at synovial sarcoma, X breakpoint 2 4.10529 206295_at interleukin 18 (interferon-gamma-inducing factor) 6.68386 205157_s_at 7.38074 202546_at vesicle-associated membrane protein 8 (endobrevin) 7.55466 205113_at neurofilament 3 (150kDa medium) 4.77986 33323_r_at stratifin 17.52384 218280_x_at H2A histone family, member O 3.24399 214455_at H2B histone family, member L 3.28328 205204_at neuromedin B 4.45710 37512_at 3-hydroxysteroid epimerase 2.05352 207666_x_at synovial sarcoma, X breakpoint 3 4.44046 214234_s_at cytochrome P450, subfamily IIIA, polypeptide 5 pseudogene 2 2.63310 209911_x_at H2B histone family, member B 2.40281 220623_s_at testis specific, 10 2.93531 204692_at leucine-rich repeat protein, neuronal 1 2.40639 205403_at interleukin 1 receptor, type II 4.81996 201422_at interferon, gamma-inducible protein 30 3.14478 205352_at serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 1 3.72141 206857_s_at FK506 binding protein 1B, 12.6 kDa 2.23166 210592_s_at spermidine/spermine N1-acetyltransferase 2.24033 214290_s_at H2A histone family, member O 3.58876 204154_at cysteine dioxygenase, type I 2.26796 210394_x_at synovial sarcoma, X breakpoint 4 5.79944 213451_x_at tenascin XB 3.85160 208436_s_at interferon regulatory factor 7 3.76645 206569_at interleukin 24 3.41736 202267_at laminin, gamma 2 2.74278 222096_x_at ESTs 2.67283 207456_at hepatocyte nuclear factor 4, gamma 5.16223 202720_at testis derived transcript (3 LIM domains) 6.92947 221651_x_at immunoglobulin kappa constant 4.64288 217522_at voltage-gated potassium channel Kv11.1 3.88715 218687_s_at mucin 13, epithelial transmembrane 3.01479 209223_at NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa 2.53835 214254_at melanoma antigen, family A, 4 15.96244 39248_at aquaporin 3 5.95019 207385_at E2F-like protein 5.61867 215189_at keratin, hair, basic, 6 (monilethrix) 2.80832 210372_s_at tumor protein D52-like 1 2.72025 213921_at somatostatin 3.23180 202790_at claudin 7 5.42806 219594_at ninjurin 2 7.46116 209581_at HRAS-like suppressor 3 2.18297 207202_s_at nuclear receptor subfamily 1, group I, member 2 2.75420 215471_s_at -associated protein 7 2.70887 205768_s_at solute carrier family 27 (fatty acid transporter), member 2 3.83710 206027_at S100 calcium binding protein A3 3.95586 205829_at hydroxysteroid (17-beta) dehydrogenase 1 3.62792 206508_at tumor necrosis factor (ligand) superfamily, member 7 3.42042 213693_s_at mucin 1, transmembrane 7.97076 209016_s_at keratin 7 4.22340 214472_at H3 histone family, member B 2.44848 202672_s_at activating transcription factor 3 2.19357 215047_at BIA2 3.92726 205186_at , axonemal, light intermediate polypeptide 1 3.58366 213954_at KIAA0888 protein 2.64326 202284_s_at cyclin-dependent kinase inhibitor 1A (p21, Cip1) 2.47866 205319_at prostate stem cell antigen 2.41314 201852_x_at collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) 3.30182 219873_at hypothetical protein MGC3279 similar to collectins 2.50927 207534_at melanoma antigen, family B, 1 3.57566 204231_s_at fatty acid amide hydrolase 2.33845 37796_at leucine-rich repeat protein, neuronal 1 2.18676 210497_x_at synovial sarcoma, X breakpoint 2 5.95374 211573_x_at transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) 2.42985 211538_s_at heat shock 70kDa protein 2 2.37024 219753_at stromal antigen 3 3.26410 216669_at Homo sapiens cDNA FLJ20286 fis, clone HEP04358 3.83392 202838_at fucosidase, alpha-L- 1, tissue 2.02138 213122_at KIAA1750 protein 2.80994 39966_at chondroitin sulfate proteoglycan 5 (neuroglycan C) 2.22051 208785_s_at ESTs, Highly similar to MPL3_HUMAN Microtubule-associated 1A/1B lig 2.14867 216080_s_at fatty acid desaturase 3 2.06554 214502_at H2B histone family, member R 2.75066 204351_at S100 calcium binding protein P 9.11595 205832_at carboxypeptidase A4 2.23813 212236_x_at keratin 17 4.79637 206504_at cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase) 2.74758 221037_s_at hypothetical protein DKFZp434N1235 3.10756 205792_at WNT1 inducible signaling pathway protein 2 5.92601 222240_s_at myo-inositol 1-phosphate synthase A1 2.37650 202843_at DnaJ (Hsp40) homolog, subfamily B, member 9 2.07322

14 Negative Significant Genes (Down-regulated Genes)

Gene ID Gene Title Fold Change 202210_x_at glycogen synthase kinase 3 alpha 0.35369 215583_at Homo sapiens cDNA FLJ12403 fis, clone MAMMA1002820 0.21899 214835_s_at succinate-CoA ligase, GDP-forming, beta subunit 0.49202 200724_at ribosomal protein L10 0.41589 211304_x_at potassium inwardly-rectifying channel, subfamily J, member 5 0.49628 216739_at Homo sapiens cDNA: FLJ20874 fis, clone ADKA02818 0.49894 218744_s_at protein kinase C and casein kinase substrate in neurons 3 0.29705 213363_at hypothetical protein PRO2325 0.40332 216886_at cholinergic receptor, nicotinic, alpha polypeptide 4 0.30455 210516_at C9orf10 protein 0.28382 216254_at parvin, beta 0.27976 214647_s_at hemochromatosis 0.48349 221320_at BCL2-like 10 (apoptosis facilitator) 0.33168 221598_s_at cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa 0.49106