Supplemental Data Table 1: Experimental Setup Correlation Array Reverse Fluor Array Extraction Coefficient Print Batch (Y/N) mean (range) DLD1-I.1 I A N DLD1-I.2 I B N 0.86 DLD1-I.3 I C N (0.79-0.90) DLD1-I.4 I C Y DLD1 DLD1-II.1 II D N DLD1-II.2 II E N 0.86 DLD1-II.3 II F N (0.74-0.94) DLD1-II.4 II F Y DLD1+3-II.1 II A N DLD1+3-II.2 II A N 0.85 DLD1 + 3 DLD1+3-II.3 II B N (0.64-0.95) DLD1+3-II.4 II B Y DLD1+7-I.1 I A N DLD1+7-I.2 I A N 0.79 DLD1 + 7 DLD1+7-I.3 I B N (0.68-0.90) DLD1+7-I.4 I B Y DLD1+13-I.1 I A N DLD1+13-I.2 I A N 0.88 DLD1 + 13 DLD1+13-I.3 I B N (0.84-0.91) DLD1+13-I.4 I B Y hTERT-HME-I.1 I A N hTERT-HME-I.2 I B N 0.85 hTERT-HME hTERT-HME-I.3 I C N (0.80-0.92) hTERT-HME-I.4 I C Y hTERT-HME+3-I.1 I A N hTERT-HME+3-I.2 I B N 0.84 hTERT-HME + 3 hTERT-HME+3-I.3 I C N (0.74-0.90) hTERT-HME+3-I.4 I C Y Supplemental Data Table 2: Average gene expression profiles by chromosome arm DLD1 hTERT-HME Ratio.7 Ratio.1 Ratio.3 Ratio.3 Chrom. Ratio.0 p.7vs0 p.13vs0 p.3vs0 Ratio.0 p.3vs0 vs0 3vs0 vs0 vs0 1p 1.00 1.04 0.0013 1.03 - 0.98 0.0293 1.00 1.02 - 1q 0.92 1.02 - 0.99 - 1.02 - 0.96 1.02 - 2p 1.03 1.05 - 1.00 - 1.00 - 1.01 0.96 0.0059 2q 0.95 1.02 - 1.01 - 0.99 - 0.99 1.01 - 3p 0.95 0.97 - 0.98 - 1.13 0.0009 0.96 1.22 <0.0001 3q 0.89 0.99 - 1.01 - 1.20 <0.0001 1.01 1.18 0.0010 4p 1.00 1.02 - 1.00 - 1.00 - 1.08 0.95 - 4q 1.05 0.96 - 0.97 - 0.97 - 1.12 0.97 - 5p 0.92 0.89 0.0411 0.98 - 1.01 - 0.89 1.05 - 5q 0.94 1.02 - 0.99 - 1.02 - 1.01 0.98 - 6p 0.88 1.08 0.0027 0.99 - 0.98 - 0.87 1.00 - 6q 1.02 1.01 - 1.06 - 1.00 - 1.06 0.91 0.0317 7p 0.95 1.14 <0.0001 0.98 - 1.00 - 0.95 1.00 - 7q 0.81 1.22 <0.0001 0.98 - 0.98 - 0.86 1.03 - 8p 0.88 1.07 0.0159 1.07 0.0063 1.04 - 1.04 0.99 - 8q 0.96 1.00 - 0.99 - 1.00 - 0.99 0.98 - 9p 1.05 1.01 - 1.02 - 0.95 - 1.10 1.01 - 9q 0.94 1.00 - 0.99 - 0.99 - 0.92 1.00 - 10p 0.90 1.04 - 1.02 - 1.04 0.0221 0.90 1.03 - 10q 1.05 1.00 - 0.98 - 0.98 - 1.08 1.01 - 11p 0.94 1.04 - 0.98 - 1.03 - 0.91 1.01 - 11q 0.92 1.00 - 0.96 - 0.98 - 0.97 0.98 - 12p 0.82 1.06 - 0.96 - 0.96 - 0.81 1.02 - 12q 0.96 1.04 0.0183 1.00 - 1.02 - 0.98 0.98 - 13q 0.99 1.01 - 1.26 0.0009 1.04 - 1.11 0.99 - 14q 0.92 1.02 - 1.01 - 1.02 - 0.93 1.00 - 15q 0.90 1.03 - 1.02 - 1.01 - 0.97 1.01 - 16p 0.93 1.05 - 0.99 - 0.97 - 0.85 1.00 - 16q 0.92 1.05 - 1.03 - 1.00 - 0.88 0.99 - 17p 1.07 1.08 - 1.00 - 0.98 - 1.05 0.98 - 17q 0.98 1.05 - 1.03 - 1.00 - 0.96 0.98 - 18p 1.03 0.96 - 1.02 - 0.97 - 1.02 0.96 - 18q 1.03 1.03 - 1.04 - 1.02 - 1.27 0.93 0.0483 19p 0.94 1.00 - 0.95 - 0.99 - 0.88 1.02 - 19q 0.93 1.03 - 0.95 - 0.98 - 0.98 1.01 - 20p 0.94 0.97 - 0.99 - 0.99 - 1.06 1.00 20q 0.84 1.02 - 1.02 - 0.99 - 0.88 1.00 21q 0.90 1.05 - 1.03 - 0.99 - 0.87 1.00 22q 0.94 1.04 - 0.98 - 0.97 - 0.91 1.00 Xp 0.89 0.97 0.0157 1.01 - 0.99 - 0.89 1.01 Xq 0.72 1.08 0.0265 0.98 - 0.98 - 0.82 1.03 Yq 1.30 0.93 - 0.99 - 0.69 <0.0001 0.97 0.96 For each chromosome arm, the average expression ratio for all genes on that arm relative to the reference RNA pool is given for the parental line (Ratio.0). The average chromosome arm expression ratios (relative to the same reference RNA for each chromosome transfer clone) are then normalized to the parental ratio value (Ratio.7vs0, Ratio.13vs0, Ratio.3vs.0) and their respective p-values from two-sample t-tests calculated. Ratio values having a p-value < 0.001 were considered significant and are in bold. P-values >0.05 are not reported. Supplemental Data Table 3: Genes significantly altered in expression in DLD1+7 a Upregulated genes Ratio.7vs0 Map Gene Description 12.40 7p21.2 TWIST twist homolog (acrocephalosyndactyly 3; Saethre-Chotzen syndrome) (Drosophila) 5.57 6p21.2 CDKN1A "cyclin-dependent kinase inhibitor 1A (p21, Cip1)" 5.16 6p21.2 CDKN1A "cyclin-dependent kinase inhibitor 1A (p21, Cip1)" 4.94 18 ESTs 4.89 Xq22.3 DSIPI "delta sleep inducing peptide, immunoreactor" 4.79 Incyte EST 4.78 4q13-q21 IL8 interleukin 8 4.68 15q26.1 IDH2 "isocitrate dehydrogenase 2 (NADP+), mitochondrial" 4.68 18q12.1 DSC2 desmocollin 2 3.99 12q13 NR4A1 "nuclear receptor subfamily 4, group A, member 1" 3.91 15q15 CKMT1 "creatine kinase, mitochondrial 1 (ubiquitous)" 3.82 22q13.1 LGALS1 "lectin, galactoside-binding, soluble, 1 (galectin 1)" 3.71 10p15-p14 AKR1C1 "aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)" 3.71 1p22 CTBS "chitobiase, di-N-acetyl-" 3.55 1p33 TSPAN-1 tetraspan 1 3.55 12q22- PAH phenylalanine hydroxylase q24.2 3.46 15q23 TSPAN-3 tetraspan 3 3.45 Xq28 ZNF185 zinc finger protein 185 (LIM domain) 3.39 Xq11-q12 HEPH hephaestin 3.35 19q13.11 FXYD3 FXYD domain containing ion transport regulator 3 3.33 1 Human hbc647 mRNA sequence. 3.32 10q25 DUSP5 dual specificity phosphatase 5 3.30 5q31.2 KIAA0416 KIAA0416 protein 3.30 14q21-q22 PYGL "phosphorylase, glycogen; liver (Hers disease, glycogen storage disease type VI)" 3.26 7q21.3- NPTX2 neuronal pentraxin II q22.1 3.21 15q23 TSPAN-3 tetraspan 3 3.15 7q32.3 SMO smoothened homolog (Drosophila) 3.14 7q21 GNAI1 "guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1" 3.13 7q21.3- NPTX2 neuronal pentraxin II q22.1 3.12 1q25.2- PTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase q25.3 and cyclooxygenase) 3.08 22q12.2 LIF leukemia inhibitory factor (cholinergic differentiation factor) 3.05 1pter- KIAA0237 KIAA0237 gene product p22.2 3.05 12p13.2- KLRC4 "killer cell lectin-like receptor subfamily C, member 4" p12.3 3.00 11p13 CD44 CD44 antigen (homing function and Indian blood group system) 2.98 7q22 TRIP6 thyroid hormone receptor interactor 6 2.97 6p25 SERPINB6 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6" 2.97 19q13.32 FOSB FBJ murine osteosarcoma viral oncogene homolog B 2.93 7p12 GBAS glioblastoma amplified sequence 2.84 17p11.2 ALDH3A2 "aldehyde dehydrogenase 3 family, member A2" 2.84 8q24.13 C8FW phosphoprotein regulated by mitogenic pathways 2.83 5q12.1- SNK serum-inducible kinase q13.2 2.82 8p12-p11 DUSP4 dual specificity phosphatase 4 2.79 1q21 MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 2.77 20q12 SDC4 "syndecan 4 (amphiglycan, ryudocan)" 2.77 17q22 ABCC3 "ATP-binding cassette, sub-family C (CFTR/MRP), member 3" 2.75 1q32.3 ATF3 activating transcription factor 3 2.74 2p21 CYP1B1 "cytochrome P450, family 1, subfamily B, polypeptide 1" 2.73 4p16 S100P S100 calcium binding protein P 2.69 7q36.1 RARRES2 retinoic acid receptor responder (tazarotene induced) 2 2.68 1p36.3 EGFL3 "EGF-like-domain, multiple 3" 2.67 10p15-p14 AKR1C4 "aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)" 2.63 2q32.1 SSFA2 sperm specific antigen 2 2.61 "trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in)" 2.61 15q13-q14 SGNE1 "secretory granule, neuroendocrine protein 1 (7B2 protein)" 2.59 16q13 MT1B metallothionein 1B (functional) 2.59 16q13 MT1E metallothionein 1E (functional) 2.56 7q22 PCOLCE procollagen C-endopeptidase enhancer 2.56 "Human DNA sequence from clone 742C19 on chromosome 22q12.3-13.1.