Comment[ArrayExpressAccession] E-GEOD-49317 MAGE-TAB Version 1.1 Public Release Date 2013-07-30 Investigation Title Affymetrix SNP array data for hepatocellular carcinoma and their adjacent liver tissue samples Comment[Submitted Name] Affymetrix SNP array data for hepatocellular carcinoma and their adjacent liver tissue samples Experiment Description Chromosomal DNA copy number alterations are a hallmark of human malignancies, including hepatocellular carcinoma (HCC). However, which oncogenes or tumor suppressors located on regions with DNA copy number aberration may contribute to HCC initiation and progression still remain obscure. Here we performed a genome-wide DNA copy number analysis on human HCC samples to identify novel potential oncogenes or tumor suppressors with DNA copy number aberrations. Genome-wide DNA copy numbers analysis was performed with single nucleotide polymorphism micoarray. RT-PCR and immunohistochemical staining were employed to evaluate the NOXIN expression in HCC samples. Colony formation, cell cycle analysis and tumor xenograft assays were performed to assess the role of NOXIN in HCC cells. Reciprocal co-immunoprecipitation experiments were used to detect the interaction between NOXIN and DNA polymerase a primase. Genome-wide DNA copy number analysis on 43 paired HCC samples indentified the smallest DNA amplification region containing NOXIN, along with the elevated transcript. NOXIN overexpression was significantly associated with HCC tumor stage. Enforced NOXIN promoted cellular proliferation, colony formation, cell migration and in vivo tumorigenicity, whereas RNA interference against NOXIN can attenuate these effects. Interestingly, NOXIN overexpression can accelerate the G1-S transition of cell cycle progression through enhancing DNA synthesis in HCC cells, as indicated by bromodeoxyuridine incorporation. Furthermore, NOXIN can interact with DNA polymerase a, implying that NOXIN may promote de novo DNA synthesis via affiliating formation of DNA polymerase-primase complex. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from hepatocellular carcinoma and adjacent liver tissue samples. Copy number analysis of Affymetrix 500K SNP arrays was performed for 43 hepatocellular carcinoma tissue samples, which their adjacent liver tissues were used as references for copy number inference. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Han Huang Han Person First Name Zeguang Jian Zeguang Person Email hangzg@chgc.sh.cn Person Affiliation Chinese National Genome Center at Shanghai Person Address Chinese National Genome Center at Shanghai, No.351,Guoshoujing Rd.,Zhangjiang Hi-Tech Park, shanghai, China Person Roles submitter Protocol Name P-GSE49317-1 P-GSE49317-3 P-GSE49317-4 P-GSE49317-2 P-GSE49317-5 Protocol Description The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. ID_REF = VALUE = Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal Signal = As per manufacturer (Affymetrix) DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions. Genomic DNA was extracted from hepatocellular carcinoma and their adjacent liver tissues using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis. The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000. Protocol Type normalization data transformation protocol labelling protocol hybridization protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name SAMPLE ID Experimental Factor Type sample id Comment[SecondaryAccession] GSE49317 Comment[GEOReleaseDate] 2013-07-30 Comment[ArrayExpressSubmissionDate] 2013-07-29 Comment[GEOLastUpdateDate] 2013-07-30 Comment[AEExperimentType] genotyping by array SDRF File E-GEOD-49317.sdrf.txt