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Sample GSM1197254 Query DataSets for GSM1197254
Status Public on Jul 30, 2013
Title HCC55N-Nsp
Sample type genomic
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma
sample id: HCC55N
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_Nsp
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 GPL3718
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-1780270 AA 0.0776011
SNP_A-1780272 NC 0.737754
SNP_A-1780285 BB 0.00841248
SNP_A-1780286 AB 0.430932
SNP_A-1780287 AA 0.00555598
SNP_A-1780289 BB 0.0418745
SNP_A-1780292 BB 0.100961
SNP_A-1780294 AA 0.00744485
SNP_A-1780295 BB 0.0828249
SNP_A-1780300 BB 0.04207
SNP_A-1780302 BB 0.00254679
SNP_A-1780303 BB 0.0307979
SNP_A-1780304 AA 0.0951658
SNP_A-1780305 BB 0.0241656
SNP_A-1780311 AA 0.122367
SNP_A-1780312 AB 0.0389762
SNP_A-1780313 BB 0.0534356
SNP_A-1780316 NC 0.827102
SNP_A-1780318 AA 0.0234856
SNP_A-1780320 AB 0.117548

Total number of rows: 262264

Table truncated, full table size 6919 Kbytes.




Supplementary file Size Download File type/resource
GSM1197254_HCC55N-Nsp.CEL.gz 19.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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