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Table S1. RT-PCR Primers Loci Forward Primer Table S2. MSP Primers 1 2 1 1 U: Primers Used to Detect Unmethylated Genomic DNA. M

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Table S1. RT-PCR Primers Loci Forward Primer Table S2. MSP Primers 1 2 1 1 U: Primers Used to Detect Unmethylated Genomic DNA. M Table S1. RT-PCR primers Loci Forward Primer Reversed Primer ER-sv 5’ ACCTTCTAGAATGTGCCTGGCTAG 5’ CTCATGCCAGGCACATTCTAGAAG ER-c 5’ ATCCACCGAGTCCTGGACAAGATC 5’ GGCACCACGTTCTTGCACTTCATG PR-1 5’ TCTCAACTACCTGAGGCCGGATTC 5’ TCCGGCCTCAGGTAGTTGAGATAG PR-2 5’ TCAGTGGGCAGATGCTGTATTT 5’ TGCGTGACATTAAGGAGAAG Kr-Znf1 5' GCGTGGAATTCACACCTGGTAAGAC 5' GTATGGTTTCTCTCCGGTGTGAAT DCC 5'ACACAGCCTGAGTTGCAAGTTCCA 5' GGACACCTCAGTGCAGAACAATCT TRIP10 5' TGATGAGGATTTCGAGGAGGAACC 5' GGGTTCAATTGAGCGTGACTCGGA MTA3 5' TGCAGGTGCCTCACAGTAGTGAAA 5' AAAGCCGTTTCCTCTCTAGGCAGA Table S2. MSP primers Primer Loci pair Detection Forward Primer Reversed Primer PR 1 U 5' CCAATAATTAAAATAAAAAAAAACTTTAAACAAA 5' TAGTTTTTATTGAGAATGTTATTTATATGTGT M 5' CGATAATTAAAATAAAAAAAAACTTTAAACGAAA 5' GTTTTTATTGAGAATGTTATTTATACGCGT 2 U 5' TGGAGATGATTGTTGTTTGTAGTAT 5' CACACAACTCCTTTATCTCCCA M 5' CGGAGATGATTGTCGTTCGTAGTA 5' CGCGACTCCTTTATCTCCCG TRIP10 1 U 5' AATTCTTTAAAAAATCAATCCAACAACATCA 5' GGTGTGTTTGGTTTTGTTTTGTTTTGTTT M 5' CTTTAAAAAATCGATCCAACGACGTCG 5' GCGTTTGGTTTCGTTTCGTTTCGTTC Kr-Znf1 1 U 5' GAGGTTGAGAAGTATAGG TTT CGTTTC 5' CGATCCGCTTCCGA TTTATACGCG M 5' GTGAGGTTGAGAAGTATAGGTTTTGTTTT 5' CACACAATCCACTTCCAAATTTATACACA U: Primers used to detect Unmethylated genomic DNA. M: Primers used to detect Methylated genomic DNA. Table S3. COBRA primers Loci Forward Primer Reversed Primer DCC 5' GGATATTTTAGTAATAAGTGAGAG 5' CAAATCATCAATAAACCACATCCAAA MTA3 5' GTTAGGGTGGTTTAGGAAGGGAGT 5' CTAAAAAACCCCCCTATAAC TACCC T PR 5' GAGGTTAAGGGTAGGAGTTGA 5' ACCCTT TACCTTCAACTCAAT Table S4. Partial list of ERα target genes identified by ChIP-on-chip Accession Chromosome Clones Loci ERE Ap1 Sp1 Description ID. Location FJ#17F9 BAIAP1 AF401654 + + + 3p14.1 MAGI-1B alpha beta mRNA FJ#20G11 DKFZP434A1022 BC033852 + + + 19q13.2 Homo sapiens, clone IMAGE:5165842, mRNA. FJ#21A12 PMPCA BC004342 + + + 19q13.2 Homo sapiens peptidase (mitochondrial processing) alpha FJ#25A5 C6orf79 BU620569 + + + 6p23 EST clone, predicted gene FJ#25A6 BRF1 BC016743 + + + 14q32.33 Transcription initiation protein IIIB, BRF1 FJ#25C8 KIAA1979 AK097037 + + + 19q13.42 Homo sapiens, Similar to zinc finger protein 268 cDNA FLJ14779 fis, moderately similar to ZINC FINGER FJ#26E3 FLJ14779 AK027685 + + + 19q13.12 PROTEIN 140 Homo sapiens breast cancer putative transcription factor FJ#26G4 ZNF217 AF041259 + + + 20q13.2 (ZABC1) mRNA FJ#30G5 FLJ39739 AK097058 - + + 1q21.1 Hypothetical protein FLJ39739 FJ#33H3 C19orf7 AB028987 + + + 19q13.32 Homo sapiens mRNA for KIAA1064 protein cDNA FLJ38524 fis, moderately similar to ZINC FINGER FJ#34B5 LOC169834 AK095843 + + + 9q33.1 PROTEIN 135 cDNA FLJ39491 fis, weakly similar to Homo sapiens Opa- FJ#39E3 OIP2 NM_181503 + + + 13q13.1 interacting protein OIP2 mRNA Similar to KRAB zinc finger protein KR18, clone FJ#40D9 MGC5384 BC028590 + + + 19q13.42 IMAGE:4827918, mRNA Human zinc finger protein (kr-znf1) mRNA, Similar to KRAB FJ#40E8 kr-znf1 CD691530 + + + 19q13.42 zinc finger protein KR18 FJ#40F3 PITX2 BC013998 + + + 4q25 Similar to paired-like homeodomain transcription factor 2, FJ#46A3 HIST1H2BG NM_003518 + + + 6p22.2 HIST1H2BG or H2BFA Homo sapiens gene SIRT3 encoding sirtuin (silent mating type FJ#46F4 SIRT3 NM_012239 + + + 11p15.5 information regulation 2 homolog) 3 FJ#47A3 MGA BC038449 + + + 7q347 Homo sapiens, Similar to MAX gene associated FJ#47D5 TRIP10 AJ000414 + + + 19p13.3 Homo sapiens mRNA for Cdc42-interacting protein 4 (CIP4) FJ#4F7 NUP155 AB018334 + + + 5p13.2 Nuclear pore complex protein Nup155 Homo sapiens mRNA; cDNA DKFZp313C088, Hypothetical FJ#50G1 MLR2 AL832106 + + + 10q24.1 protein DKFZp313C088 Homo sapiens BRCA1-binding helicase-like protein BACH1 FJ#58B5 BRIP1 AF360549 + + + 17q23.2 mRNA FJ#5B3 DCC X76132 - + + 18q21.2 H.sapiens DCC mRNA .
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