Supplementary Fig. S1. Woloszynska-Read et al.
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1 Supplementary Fig. S1. Woloszynska-Read et al. A % BORIS Methylat tion Normal Ovary P<.1 EOC B % MAGE-A1 methyl lation Normal Ovary P<.1 EOC C D % XAGE E-1 methylation P<.1 P=.4 Normal Ovary EOC % NY-ES SO-1 methylation Normal Ovary EOC
2 Supplementary Fig. S2. Woloszynska-Read et al. 7A EOC 7 EOC 13 EOC 38 EOC 39 EOC EOC 42 EOC 47 EOC 48 EOC 49 EOC 5 EOC 51 EOC 55 EOC 57 EOC 59 EOC 7 EOC 71 EOC 77 EOC 83 EOC 85 97KDa 64KDa BORIS 51KDa 97KDa CTCF 39KDa Actin B C 8. P=.6 P=.4 BORIS/Actin Protein (arbitrary units) CTCF/Actin Protein (arbitrary units) BORIS/GAPDH mrna copy number CTCF/GAPDH mrna copy number
3 Supplementary Table S1. Sample Characteristics Sample Number Age Primary Tumor Grade Stage Histology EOC1 44 OVARY 3 IIIC SEROUS EOC2 79 OVARY 3 IIIC SEROUS EOC3 68 OVARY 3 IIIC SEROUS EOC5 77 OVARY 3 IIIC SEROUS EOC7 73 PRIMARY PERITONEAL 3 IV SEROUS EOC8 88 OVARY 3 IIIC CARCINOSARCOMA EOC1 56 PRIMARY PERITONEAL & PANCREATIC 3 IIIC SEROUS EOC11 81 OVARY 3 IIIB SEROUS EOC12 49 OVARY 3 IIIC SEROUS EOC13 54 OVARY 3 IV MIXED EOC14 73 OVARY 3 IV SEROUS EOC15 67 OVARY 3 N/D SEROUS EOC16 57 PRIMARY PERITONEAL 3 IIIC SEROUS EOC17 58 PRIMARY PERITONEAL 3 IV SEROUS EOC18 36 OVARY 3 IIIC SEROUS EOC19 57 OVARY 2 IIB SEROUS EOC28 7 OVARY 3 IV SEROUS EOC31 53 PRIMARY PERITONEAL 3 IIIC SEROUS EOC32 46 OVARY 3 IC SEROUS EOC35 38 OVARY 1 IIB MUCINOUS EOC37 51 OVARY 3 IC CLEAR EOC38 67 OVARY 3 IV MIXED EOC39 62 OVARY 3 IV SEROUS EOC 67 OVARY 3 IIIC CARCINOSARCOMA EOC41 66 OVARY 2 IIIC MUCINOUS EOC42 63 PRIMARY PERITONEAL 3 IIIC SEROUS EOC43 78 OVARY 3 IIIC SEROUS EOC44 48 OVARY 3 IIIC SEROUS EOC45 52 OVARY 2 IC ENDOMETRIOID EOC47 46 PRIMARY PERITONEAL 2 IIIC SEROUS EOC48 65 OVARY N/D IIB GRANULOSA EOC49 48 OVARY 3 IIIC SEROUS EOC5 75 PRIMARY PERITONEAL 3 IIIC SEROUS EOC51 58 OVARY 3 IIB CLEAR EOC52 7 PRIMARY PERITONEAL 3 IIIC SEROUS EOC53 68 OVARY N/D N/D N/D EOC54 74 PRIMARY PERITONEAL 3 IIIC SEROUS EOC55 OVARY 3 IIIC SEROUS EOC56 78 OVARY 3 IIIC PNET EOC57 51 OVARY 3 IIIC SEROUS EOC58 28 OVARY 2 IA IMMATURE TERATOMA EOC59 71 PRIMARY PERITONEAL 3 IIIC SEROUS EOC 82 OVARY 3 IIIC SEROUS EOC63 51 OVARY 3 IIIC CLEAR EOC64 62 OVARY 3 IIIC SEROUS EOC65 73 OVARY 3 N/D SEROUS EOC66 47 OVARY 3 IIIC SEROUS EOC67 42 OVARY 3 IIIC SEROUS EOC68 44 OVARY 3 IIIC SEROUS EOC69 59 OVARY 3 IIIC MIXED EOC7 55 OVARY 3 IIB CLEAR EOC71 62 OVARY 3 IIIC SEROUS EOC72 73 OVARY 2 IIIC MUCINOUS EOC73 57 OVARY 3 IIIC SEROUS EOC74 62 OVARY 3 IIIC SEROUS
4 EOC75 83 OVARY 2 IIC MUCINOUS EOC76 56 OVARY 1 IA MUCINOUS EOC77 64 PRIMARY PERITONEAL 3 IIIC SEROUS EOC82 65 PRIMARY PERITONEAL 3 IV SEROUS EOC83 75 OVARY 3 IIIC MIXED EOC84 71 OVARY 3 IIC SEROUS EOC85 64 OVARY 3 IIIC SEROUS EOC86 68 OVARY 2 IIIC SEROUS EOC87 59 OVARY 2 IIIC SEROUS EOC89 73 OVARY 3 IIIC SEROUS EOC9 56 OVARY 3 IIC CLEAR EOC91 67 OVARY 3 IIIC SEROUS EOC93 69 OVARY 3 IIIB CARCINOSARCOMA EOC94 54 OVARY 3 IIIC SEROUS EOC95 64 OVARY 3 IIIC SEROUS EOC96 76 OVARY 3 IIIC SEROUS EOC97 69 OVARY 3 IIIC CARCINOSARCOMA EOC98 89 OVARY 3 IIIC SEROUS EOC99 26 PRIMARY PERITONEAL 3 IIIB SEROUS EOC 84 OVARY 3 IIIC CARCINOSARCOMA EOC11 29 OVARY 3 IIIC SEROUS N/D = not determined
5 Supplementary Table S2. Gene information Gene Name Accession # or Chromosome Gene Repetitive Element 5' CpG island CpG island size, Pyrosequencing # CpG sites Gene ID Location Size (bp) Locations 1 Location 2 %GC, Obs/Exp 3 Primer Locations analyzed LINE-1 X all 1147 N/A N/A N/A 794, Alu Sx U all 29 N/A 1 to , 61%, , Sat- a AJ all 535 N/A N/A N/A 1, MAGE-A1 GID 4 Xq (A) -189 to , 65%, , NY-ESO-1 GID 1485 Xq (L), -191 (L) -369 to , 71%, , XAGE-1B GID 953 Xp (A), -391 (A) -7 to , 58%,.59-7, BORIS/CTCFL GID 169 q (L) -4 to , 72%,.53-22, SOHLH2 GID q (A), -55 (A), +18 (A) -469 to , 61%, , -127; -1, Note: Sequence element locations are reported relative to the transcriptional start site (TSS) for single copy genes 1 Within +/- 2kb of the TSS. Determined using the UCSC genome browser ( (L) = LINE-1, (A) = Alu 2 Determined using Webgene ( 3 Determined using Webgene and the CpG ratio and GC content Plotter (
6 Supplementary Table S3. Summmary Statistics of Molecular Data Variable Measurement Type N Mean SD Median Min Max BORIS mrna Gene expression E BORIS/CTCF mrna " CTCF mrna " MAGE-A1 mrna " E NY-ESO-1 mrna " E XAGE-1 mrna " BORIS methylation Promoter methylation MAGE-A1 methylation " NY-ESO-1 methylation " SOHLH2 methylation " XAGE-1 methylation " % 5mdC/dG Global methylation LINE-1 methylation " Alu Sx methylation " Sat- a methylation " mrna expression (copy number) was measured by qrt-pcr and is normalized to GAPDH mrna 2 Promoter methylation was determined by sodium bisulfite pyrosequencing (data = % methylation) 3 Global methylation was determined by sodium bisulfite pyrosequencing (data = % methylation), except % 5mdC, which was measured by LC-MS
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