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Sample GSM1197301 Query DataSets for GSM1197301
Status Public on Jul 30, 2013
Title HCC67N-Sty
Sample type genomic
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma
sample id: HCC67N
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 BB 0.122381
SNP_A-1780274 AA 0.0414944
SNP_A-1780277 AB 0.00845017
SNP_A-1780278 BB 0.132999
SNP_A-1780283 BB 0.136548
SNP_A-1780290 AA 0.0168622
SNP_A-1780293 BB 0.0197504
SNP_A-1780299 BB 3.43E-05
SNP_A-1780301 BB 0.0502643
SNP_A-1780310 AA 0.0905759
SNP_A-1780315 AA 0.128879
SNP_A-1780317 AB 0.070858
SNP_A-1780319 BB 0.00945274
SNP_A-1780324 AB 0.00267717
SNP_A-1780325 AB 0.0360775
SNP_A-1780328 AA 0.0600337
SNP_A-1780333 AB 0.00724951
SNP_A-1780335 AB 0.0198384
SNP_A-1780339 BB 0.0136399
SNP_A-1780340 AB 0.279145

Total number of rows: 238304

Table truncated, full table size 6281 Kbytes.




Supplementary file Size Download File type/resource
GSM1197301_HCC67N-Sty.CEL.gz 20.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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