Supplementary Table S2. Differential Expression of DNA Damage Response Genes in FT282-CCNE1 Cells Compared to FT282-V Cells

Supplementary Table S2. Differential expression of DNA damage response genes in FT282-CCNE1 cells compared to FT282-V cells.

Gene Fold Target Refseq Gene name P-value* Note symbol change 1 NM_005157 ABL1 C-abl oncogene 1, non-receptor tyrosine -1.4769 0.001218 kinase 2 NM_080649 APEX1 APEX nuclease (multifunctional DNA 1.043 0.060722 repair enzyme) 1 3 NM_000051 ATM Ataxia telangiectasia mutated -3.5208 0.000101 4 NM_001184 ATR Ataxia telangiectasia and Rad3 related 1.2723 0.021095 5 NM_032166 ATRIP ATR interacting protein 1.1361 0.028965 6 NM_000489 ATRX Alpha thalassemia/mental retardation -1.4498 0.000062 syndrome X-linked 7 NM_000465 BARD1 BRCA1 associated RING domain 1 1.1335 0.08649 8 NM_004324 BAX BCL2-associated X protein -2.0838 0.000061 9 NM_014417 BBC3 BCL2 binding component 3 -7.8312 0.000012 10 NM_000057 BLM Bloom syndrome, RecQ helicase-like 2.015 0.000093 11 NM_007294 BRCA1 Breast cancer 1, early onset 2.3415 0.000391 12 NM_032043 BRIP1 BRCA1 interacting protein C-terminal 1.0773 0.269005 helicase 1 13 NM_001789 CDC25A Cell division cycle 25 homolog A (S. 1.6067 0.001764 pombe) 14 NM_001790 CDC25C Cell division cycle 25 homolog C (S. 2.7845 0.000025 pombe) 15 NM_001799 CDK7 Cyclin-dependent kinase 7 -1.1507 0.023729 16 NM_000389 CDKN1A Cyclin-dependent kinase inhibitor 1A -6.0317 0.000017 (p21, Cip1) 17 NM_001274 CHEK1 CHK1 checkpoint homolog (S. pombe) -1.222 0.005004 18 NM_007194 CHEK2 CHK2 checkpoint homolog (S. pombe) 1.2723 0.0304 19 NM_006384 CIB1 Calcium and integrin binding 1 (calmyrin) -1.4975 0.000385 20 NM_004075 CRY1 Cryptochrome 1 (photolyase-like) -1.6349 0.001562 21 NM_001896 CSNK2A2 Casein kinase 2, alpha prime polypeptide -1.2506 0.007022 22 NM_001923 DDB1 Damage-specific DNA binding protein 1, 1.1335 0.022962 127kDa 23 NM_000107 DDB2 Damage-specific DNA binding protein 2, -2.4103 0.00002 48kDa 24 NM_004083 DDIT3 DNA-damage-inducible transcript 3 1.3417 0.037144 25 NM_001983 ERCC1 Excision repair cross-complementing -1.1695 0.022032 rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence) 26 NM_000400 ERCC2 Excision repair cross-complementing -1.1349 0.0036 rodent repair deficiency, complementation group 2 27 NM_130398 EXO1 Exonuclease 1 1.1076 0.220677 28 NM_000135 FANCA Fanconi anemia, complementation group A 1.1816 0.007017 29 NM_033084 FANCD2 Fanconi anemia, complementation group 2.3307 0.000101 D2 30 NM_004629 FANCG Fanconi anemia, complementation group G 1.5919 0.000451 31 NM_004111 FEN1 Flap structure-specific endonuclease 1 1.603 0.000296 32 NM_001924 GADD45A Growth arrest and DNA-damage- -1.3372 0.008626 inducible, alpha 33 NM_006705 GADD45G Growth arrest and DNA-damage- -2.2026 0.000285 A inducible, gamma 34 NM_002105 H2AFX H2A histone family, member X 1.5235 0.000289 35 NM_004507 HUS1 HUS1 checkpoint homolog (S. pombe) 1.1076 0.001018 36 NM_000234 LIG1 Ligase I, DNA, ATP-dependent -1.1349 0.078527 37 NM_002969 MAPK12 Mitogen-activated protein kinase 12 -2.0935 0.000012 38 NM_003925 MBD4 Methyl-CpG binding domain protein 4 -1.0395 0.350397 39 NM_024596 MCPH1 Microcephalin 1 1.0576 0.267273 40 NM_014641 MDC1 Mediator of DNA-damage checkpoint 1 1.7663 0.00001 41 NM_000249 MLH1 MutL homolog 1, colon cancer, 1.3987 0.00106 nonpolyposis type 2 (E. coli) 42 NM_014381 MLH3 MutL homolog 3 (E. coli) 1.4514 0.015612 43 NM_002434 MPG N-methylpurine-DNA glycosylase -2.9812 0.000001 44 NM_005590 MRE11A MRE11 meiotic recombination 11 -1.4135 0.00133 homolog A (S. cerevisiae) 45 NM_000251 MSH2 MutS homolog 2, colon cancer, -1.1561 0.013755 nonpolyposis type 1 (E. coli) 46 NM_002439 MSH3 MutS homolog 3 (E. coli) -1.1064 0.009537 47 NM_002485 NBN Nibrin -1.2248 0.012315 48 NM_002528 NTHL1 Nth endonuclease III-like 1 (E. coli) -1.4332 0.001889 49 NM_002542 OGG1 8-oxoguanine DNA glycosylase 1.1654 0.27832 50 NM_001618 PARP1 Poly (ADP-ribose) polymerase 1 -1.394 0.000306 51 NM_182649 PCNA Proliferating cell nuclear antigen -1.2506 0.000741 52 NM_000534 PMS1 PMS1 postmeiotic segregation increased 1 -1.1804 0.020604 (S. cerevisiae) 53 NM_000535 PMS2 PMS2 postmeiotic segregation increased 2 1.0122 0.679765 (S. cerevisiae) 54 NM_007254 PNKP Polynucleotide kinase 3'-phosphatase -1.1219 0.086128 55 NM_003620 PPM1D Protein phosphatase, Mg2+/Mn2+ -1.6693 0.000055 dependent, 1D 56 NM_014330 PPP1R15A Protein phosphatase 1, regulatory 1.1102 0.01822 (inhibitor) subunit 15A 57 NM_006904 PRKDC Protein kinase, DNA-activated, catalytic 1.305 0.002488 polypeptide 58 NM_002853 RAD1 RAD1 homolog (S. pombe) 1.2177 0.010524 59 NM_002873 RAD17 RAD17 homolog (S. pombe) 1.1898 0.011447 60 NM_020165 RAD18 RAD18 homolog (S. cerevisiae) 1.4514 0.001535 61 NM_006265 RAD21 RAD21 homolog (S. pombe) 1.4215 0.000434 62 NM_005732 RAD50 RAD50 homolog (S. cerevisiae) -1.0492 0.085718 63 NM_002875 RAD51 RAD51 homolog (S. cerevisiae) 1.5165 0.000451 64 NM_133509 RAD51B RAD51 homolog B (S. cerevisiae) 1.8202 0.000742 65 NM_004584 RAD9A RAD9 homolog A (S. pombe) 1.2519 0.004042 66 NM_002894 RBBP8 Retinoblastoma binding protein 8 -1.0111 0.340985 67 NM_016316 REV1 REV1 homolog (S. cerevisiae) -1.3559 0.004764 68 NM_152617 RNF168 Ring finger protein 168 -1.1193 0.038097 69 NM_183078 RNF8 Ring finger protein 8 1.305 0.001386 70 NM_002945 RPA1 Replication protein A1, 70kDa 1.2037 0.004157 71 NM_012238 SIRT1 Sirtuin 1 -1.1271 0.031498 72 NM_006306 SMC1A Structural maintenance of chromosomes 1.1627 0.000939 1A 73 NM_003352 SUMO1 SMT3 suppressor of mif two 3 homolog 1 1.0168 0.775216 (S. cerevisiae) 74 NM_007027 TOPBP1 Topoisomerase (DNA) II binding protein 1 1.4615 0.000404 75 NM_000546 TP53 Tumor protein p53 3.2583 0.000012 76 NM_005657 TP53BP1 Tumor protein p53 binding protein 1 -1.0638 0.043038 77 NM_005427 TP73 Tumor protein p73 -3.8439 0.081694 B 78 NM_003362 UNG Uracil-DNA glycosylase 1.0239 0.654155 79 NM_000380 XPA Xeroderma pigmentosum, -1.3812 0.009756 complementation group A 80 NM_004628 XPC Xeroderma pigmentosum, -1.9175 0.001752 complementation group C 81 NM_006297 XRCC1 X-ray repair complementing defective 1.0999 0.055314 repair in Chinese hamster cells 1 82 NM_005431 XRCC2 X-ray repair complementing defective 2.3307 0.001179 repair in Chinese hamster cells 2 83 NM_005432 XRCC3 X-ray repair complementing defective 1.8542 0.004151 repair in Chinese hamster cells 3 84 NM_001469 XRCC6 X-ray repair complementing defective 1.3891 0.000105 repair in Chinese hamster cells 6

*P-values were calculated based on a Student’s t-test of the replicate 2^(- Delta Ct) values for each gene in the control group and treatment groups. P-values less than 0.05 are indicated in red.

Comment A: This gene’s average threshold cycle is relatively high (> 30) in either the control or the test sample, and is reasonably low in the other sample (< 30). These data mean that the gene’s expression is relatively low in one sample and reasonably detected in the other sample suggesting that the actual fold-change value is at least as large as the calculated and reported fold-change result.

Comment B: This gene’s average threshold cycle is relatively high (> 30), meaning that its relative expression level is low, in both control and test samples, and the p-value for the fold-change is either unavailable or relatively high (P > 0.05). This fold-change result may also have greater variations; therefore, it is important to have a sufficient number of biological replicates to validate the result for this gene.