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Sample GSM1197294 Query DataSets for GSM1197294
Status Public on Jul 30, 2013
Title HCC49N-Sty
Sample type genomic
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma
sample id: HCC49N
Extracted molecule genomic DNA
Extraction protocol 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.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to 250K_Sty
Data processing 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.
 
Submission date Jul 29, 2013
Last update date Jul 30, 2013
Contact name Zeguang Han
E-mail(s) hangzg@chgc.sh.cn
Organization name Chinese National Genome Center at Shanghai
Street address No.351,Guoshoujing Rd.,Zhangjiang Hi-Tech Park
City shanghai
ZIP/Postal code 201203
Country China
 
Platform ID GPL3720
Series (1)
GSE49317 Affymetrix SNP array data for hepatocellular carcinoma and their adjacent liver tissue samples

Data table header descriptions
ID_REF
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Signal

Data table
ID_REF VALUE Signal
SNP_A-1780271 NC 0.668
SNP_A-1780274 AA 0.049695
SNP_A-1780277 AA 0.113527
SNP_A-1780278 BB 0.452041
SNP_A-1780283 AB 0.0471985
SNP_A-1780290 BB 0.146483
SNP_A-1780293 BB 0.178776
SNP_A-1780299 AA 0.120234
SNP_A-1780301 BB 0.036638
SNP_A-1780310 AA 0.0298836
SNP_A-1780315 AA 0.0626085
SNP_A-1780317 BB 0.328426
SNP_A-1780319 BB 0.0296927
SNP_A-1780324 BB 0.0029318
SNP_A-1780325 AB 0.0322415
SNP_A-1780328 AA 0.0589157
SNP_A-1780333 AA 0.146118
SNP_A-1780335 BB 0.166299
SNP_A-1780339 BB 0.101024
SNP_A-1780340 AA 0.182407

Total number of rows: 238304

Table truncated, full table size 6198 Kbytes.




Supplementary file Size Download File type/resource
GSM1197294_HCC49N-Sty.CEL.gz 28.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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