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Supplementary Figure S1 A Supplementary Figure S1 A B C 1 4 1 3 1 2 1 2 1 0 1 1 (Normalized signal values)] 2 (Normalized signal values) (Normalized 8 2 10 Log 6 AFFX-BioC AFFX-BioB AFFX-BioDn AFFX-CreX hDFs [Log 6 8 10 12 14 hOFs [Log2 (Normalized signal values)] Supplementary Figure S2 GLYCOLYSIS PENTOSE-PHOSPHATE PATHWAY Glucose Purine/pyrimidine Glucose-6-phosphate metabolism AMINO ACID Fluctose-6-phosphate AMPK METABOLISM TIGAR PFKFB2 methylgloxal GloI Ser, Gly, Thr Glyceraldehyde-3-phosphate ALDH Lactate PYRUVATE LDH METABOLISM acetic acid Ethanol Pyruvate GLYCOSPHINGOLIPID NADH BIOSYNTHESIS Ala, Cys DLD PDH PDK3 DLAT Fatty acid Lys, Trp, Leu, Acetyl CoA ACAT2 Ile, Tyr, Phe β-OXIDATION ACACA Citrate Asp, Asn Citrate Acetyl CoA Oxaloacetate Isocitrate MDH1 IDH1 Glu, Gln, His, ME2 TCA Pro, Arg 2-Oxoglutarate MDH1 CYCLE Pyruvate Malate ME2 GLUTAMINOLYSIS FH Succinyl-CoA Fumalate SUCLA2 Tyr, Phe Var, Ile, Met Supplementary Figure S3 Entrez Gene Symbol Gene Name hODs hDFs hOF-iPSCs GeneID 644 BLVRA biliverdin reductase A 223.9 259.3 253.0 3162 HMOX1 heme oxygenase 1 1474.2 2698.0 452.3 9365 KL klotho 54.1 44.8 36.5 nicotinamide 10135 NAMPT 827.7 626.2 2999.8 phosphoribosyltransferase nuclear factor (erythroid- 4780 NFE2L2 2134.5 1331.7 1006.2 derived 2) related factor 2 peroxisome proliferator- 5467 PPARD 1534.6 1352.9 330.8 activated receptor delta peroxisome proliferator- 5468 PPARG 524.4 100.8 63.0 activated receptor gamma 5621 PRNP prion protein 4059.0 3134.1 1065.5 5925 RB1 retinoblastoma 1 882.9 805.8 739.3 23411 SIRT1 sirtuin 1 231.5 216.8 1676.0 7157 TP53 tumor protein p53 2107.7 2197.0 2149.1 Supplementary Figure S4 Entrez Expresse Gene hOF- Location Gene Name hOFs hDFs Gene ID d Allele Symbol iPSCs DIRAS family, GTP- 9077 Paternal 1p31 AS DIRAS3 254.9 140.7 72.4 binding RAS-like 3 23089 Paternal 7q21 PEG10 paternally expressed 10 257.1 374.8 1841.9 H19, imprinted maternally 11p15.5 283120 Maternal H19 expressed transcript (non- 1304.4 801.3 559.8 AS protein coding) 11p15.5 insulin-like growth factor 2 3481 Paternal IGF2 1060.0 184.8 82.6 AS (somatomedin A) potassium voltage-gated 3784 Maternal 11p15.5 KCNQ1 channel, KQT-like 150.2 147.2 107.9 subfamily, member 1 maternally expressed 3 55384 Maternal 14q32 MEG3 738.9 418.8 476.7 (non-protein coding) 8788 Paternal 14q32 DLK1 delta-like 1 homolog 161.4 182.5 173.5 14q32.31 388015 Paternal RTL1 retrotransposon-like 1 78.9 79.0 68.7 AS deiodinase, iodothyronine, 1735 Paternal 14q32 Dio3 76.5 84.5 68.6 type III maternally expressed 8 79104 Maternal 14q32.31 MEG8 n.d. n.d. n.d. (non-protein coding) 15q11.2- 4692 Paternal NDN necdin homolog (mouse) 147.2 122.5 98.9 q12 AS 19q13.4 5178 Paternal PEG3 paternally expressed 3 104.5 107.8 86.7 AS Supplementary Table S1. 12,713 gene probe list after differential expression analysis with One-way ANOVA (corrected p < 0.05). Transcripts Gene hOF- corrected p- Entrez Gene Gene description hOFs hDFs p-value Cluster Id symbol iPSCs value (BH) 7980908 10516 fibulin 5 FBLN5 13.59 13.13 7.99 1.86E-11 5.37E-07 7899167 79727 lin-28 homolog A (C. elegans) LIN28A 6.59 6.60 12.95 6.80E-11 9.81E-07 solute carrier family 7 (cationic amino acid transporter, 8173414 84889 SLC7A3 5.97 6.02 12.94 1.98E-10 9.88E-07 y+ system), member 3 7969533 122060 SLAIN motif family, member 1 SLAIN1 5.61 5.41 10.02 2.05E-10 9.88E-07 8102404 407028 microRNA 302a MIR302A 4.52 4.53 11.09 1.22E-10 9.88E-07 5460, 642559, 8178470 POU class 5 homeobox 1 POU5F1 7.34 7.30 13.19 1.67E-10 9.88E-07 645682, 5462 8170648 633 biglycan BGN 13.48 13.57 7.57 2.53E-10 1.04E-06 8041853 4072 epithelial cell adhesion molecule EPCAM 5.42 5.50 12.02 7.89E-10 2.85E-06 8052940 400961 poly(A) binding protein interacting protein 2B PAIP2B 6.37 6.36 9.97 9.95E-10 2.87E-06 8102406 442894 microRNA 302b MIR302B 4.50 4.51 11.33 9.53E-10 2.87E-06 chromosome 13 open reading frame 38 | 728591, C13orf38 7970989 spermatogenesis and oogenesis specific basic helix- 6.04 6.20 10.83 1.14E-09 3.00E-06 54937 |SOHLH2 loop-helix 2 8169385 6998 teratocarcinoma-derived growth factor 3, pseudogene TDGF3 5.97 6.12 10.61 1.57E-09 3.50E-06 5460, 642559, 8124889 POU class 5 homeobox 1 POU5F1 7.13 7.10 12.71 1.62E-09 3.50E-06 645682, 5462 5460, 642559, 8179719 POU class 5 homeobox 1 POU5F1 7.11 7.09 12.71 1.70E-09 3.50E-06 645682, 5462 8089438 151871 developmental pluripotency associated 2 DPPA2 4.97 4.94 9.12 2.27E-09 4.37E-06 8072015 157 adrenergic, beta, receptor kinase 2 ADRBK2 5.91 5.86 9.25 2.93E-09 4.46E-06 7962455 4753 NEL-like 2 (chicken) NELL2 5.35 5.29 9.28 2.79E-09 4.46E-06 sortilin-related receptor, L(DLR class) A repeats- 7944667 6653 SORL1 6.32 6.44 10.00 2.55E-09 4.46E-06 containing NANOG 79923, 7953675 Nanog homeobox | Nanog homeobox pseudogene 1 |NANOGP 6.32 6.28 12.18 2.88E-09 4.46E-06 404635 1 7996837 999 cadherin 1, type 1, E-cadherin (epithelial) CDH1 6.22 6.22 11.45 3.09E-09 4.46E-06 8162652 1515 cathepsin L2 CTSL2 5.30 5.36 9.06 3.44E-09 4.73E-06 8077366 57633 leucine rich repeat neuronal 1 LRRN1 5.04 5.06 11.62 4.09E-09 5.19E-06 8044878 4.48 4.48 5.20 4.13E-09 5.19E-06 7986822 2562 gamma-aminobutyric acid (GABA) A receptor, beta 3 GABRB3 7.12 7.17 10.87 4.95E-09 5.50E-06 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, 8160637 2683 B4GALT1 10.85 11.37 8.04 4.92E-09 5.50E-06 polypeptide 1 7932109 22929 selenophosphate synthetase 1 SEPHS1 10.69 10.36 13.17 4.87E-09 5.50E-06 8098745 654254 zinc finger protein 732 ZNF732 5.57 5.51 8.65 5.97E-09 6.16E-06 50848, F11 receptor | thiosulfate sulfurtransferase F11R|TST 7921713 6.79 6.81 11.09 5.86E-09 6.16E-06 100131187 (rhodanese)-like domain containing 1 D1 8089448 55211 developmental pluripotency associated 4 DPPA4 5.84 5.74 11.70 6.30E-09 6.27E-06 immunoglobulin superfamily containing leucine-rich 7984813 3671 ISLR 12.42 12.64 6.40 7.29E-09 6.52E-06 repeat protein tyrosine phosphatase, receptor-type, Z 8135774 5803 PTPRZ1 5.28 5.24 11.23 7.01E-09 6.52E-06 polypeptide 1 8100464 10874 neuromedin U NMU 5.54 5.61 8.93 6.98E-09 6.52E-06 8148040 114569 mal, T-cell differentiation protein 2 MAL2 6.11 6.04 12.90 7.46E-09 6.52E-06 8134263 1278 collagen, type I, alpha 2 COL1A2 13.26 13.37 8.83 7.95E-09 6.75E-06 7965565 84101 ubiquitin specific peptidase 44 USP44 5.54 5.86 11.63 8.35E-09 6.89E-06 8121251 389421 lin-28 homolog B (C. elegans) LIN28B 4.78 4.68 9.34 9.02E-09 7.23E-06 7923582 6.21 6.69 9.27 1.00E-08 7.83E-06 8069668 116159 cysteine/tyrosine-rich 1 CYYR1 6.27 6.29 10.23 1.14E-08 8.65E-06 8016646 1277 collagen, type I, alpha 1 COL1A1 13.68 13.78 9.54 1.31E-08 9.24E-06 8020779 1829 desmoglein 2 DSG2 5.12 5.06 10.83 1.36E-08 9.24E-06 8129783 9053 microtubule-associated protein 7 MAP7 7.03 6.90 10.13 1.40E-08 9.24E-06 8133976 10926 DBF4 4.75 4.91 6.91 1.42E-08 9.24E-06 7927631 22943 dickkopf homolog 1 (Xenopus laevis) DKK1 10.71 12.13 6.02 1.44E-08 9.24E-06 8111524 167127 UDP glycosyltransferase 3 family, polypeptide A2 UGT3A2 6.48 6.19 10.34 1.30E-08 9.24E-06 79923, NANOG|N 7987365 Nanog homeobox | Nanog homeobox pseudogene 1 6.54 6.40 11.82 1.37E-08 9.24E-06 404635 ANOGP1 8035855 148213 zinc finger protein 681 ZNF681 5.59 5.40 8.69 1.54E-08 9.64E-06 8046003 25801 grancalcin, EF-hand calcium binding protein GCA 5.19 4.81 8.60 1.65E-08 1.01E-05 matrix metallopeptidase 2 (gelatinase A, 72kDa 7995681 4313 MMP2 13.34 13.54 9.11 1.71E-08 1.02E-05 gelatinase, 72kDa type IV collagenase) 8167185 7076 TIMP metallopeptidase inhibitor 1 TIMP1 13.81 13.86 11.29 1.75E-08 1.02E-05 8133983 53616 ADAM metallopeptidase domain 22 ADAM22 5.14 5.29 7.19 1.77E-08 1.02E-05 carbohydrate (N-acetylgalactosamine 4-0) 8022666 83539 CHST9 5.32 5.29 8.17 1.84E-08 1.03E-05 sulfotransferase 9 8089988 131076 coiled-coil domain containing 58 CCDC58 7.11 7.39 9.63 1.86E-08 1.03E-05 7955869 3224 homeobox C8 HOXC8 6.91 10.08 6.28 1.93E-08 1.05E-05 8033767 147741 zinc finger protein 560 ZNF560 6.54 5.55 10.02 2.03E-08 1.08E-05 small nuclear ribonucleoprotein D3 polypeptide 18kDa SNRPD3|C 8071920 6634, 83606 8.14 8.16 10.18 2.05E-08 1.08E-05 | chromosome 22 open reading frame 13 22orf13 8179041 3105 major histocompatibility complex, class I, A HLA-A 13.34 13.17 11.36 2.17E-08 1.10E-05 8000574 26471 nuclear protein, transcriptional regulator, 1 NUPR1 12.59 12.48 7.18 2.16E-08 1.10E-05 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, 8046078 8708 B3GALT1 5.47 5.23 10.60 2.45E-08 1.20E-05 polypeptide 1 8020806 54941 ring finger protein 125 RNF125 5.46 5.45 9.19 2.45E-08 1.20E-05 8115691 6586 slit homolog 3 (Drosophila) SLIT3 12.61 12.72 6.58 2.53E-08 1.22E-05 8147351 54845 epithelial splicing regulatory protein 1 ESRP1 5.66 5.90 11.38 2.60E-08 1.23E-05 LOC44166 8045330 441666 zinc finger protein 91 pseudogene 4.64 4.60 6.56 2.67E-08 1.25E-05 6 8171359 2824 glycoprotein M6B GPM6B 5.48 5.49 9.47 3.17E-08 1.38E-05 7980152 4053 latent transforming growth factor beta binding protein 2 LTBP2 11.85 12.51 6.74 3.25E-08 1.38E-05 nuclear factor I/X (CCAAT-binding transcription 8026139 4784 NFIX 11.54 11.60 7.05 3.10E-08 1.38E-05 factor) 8097017 7368 UDP glycosyltransferase 8 UGT8 5.89 5.78 9.96 3.08E-08 1.38E-05 7998898 9074 claudin 6 CLDN6 6.29 6.34 12.57 3.21E-08 1.38E-05 cysteine-rich secretory protein LCCL domain 8146967 83690 CRISPLD1 5.45 5.31 9.12 3.16E-08 1.38E-05 containing 1 8138805 54504 carboxypeptidase, vitellogenic-like CPVL 6.08 5.98 8.52 3.33E-08 1.39E-05 8108217 7045 transforming growth factor, beta-induced, 68kDa TGFBI 13.46 13.68 8.32 3.39E-08 1.40E-05 7996819 1001 cadherin 3, type 1, P-cadherin (placental) CDH3 6.23 6.24 11.23 3.46E-08 1.41E-05 7960744 715 complement component 1, r subcomponent C1R 12.84 12.14 7.67 3.69E-08 1.46E-05 8006187 79915 ATPase family, AAA domain containing 5 ATAD5 5.42 5.42 8.62 3.69E-08 1.46E-05 major histocompatibility complex, class I, C | major HLA- 8124901 3107, 3106 12.78 12.55 10.89 3.90E-08 1.52E-05 histocompatibility complex, class I, B C|HLA-B 8170200 7547 Zic family member 3 (odd-paired homolog, Drosophila) ZIC3 5.76 5.94 10.18 3.96E-08 1.53E-05 solute carrier family 16, member 10 (aromatic amino 8121515 117247 SLC16A10 6.31 6.27 10.36 4.10E-08 1.56E-05 acid transporter) 8067955 1525 coxsackie virus and adenovirus receptor CXADR 6.58 6.51 12.49 4.29E-08 1.59E-05 mutS homolog 2, colon cancer, nonpolyposis type 1 (E.
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