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Sample GSM1197269 Query DataSets for GSM1197269
Status Public on Jul 30, 2013
Title HCC109N-Sty
Sample type genomic
 
Source name hepatocellular carcinoma
Organism Homo sapiens
Characteristics disease state: hepatocellular carcinoma
sample id: HCC109N
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 0.991452
SNP_A-1780274 AB 0.00642489
SNP_A-1780277 AB 0.00199349
SNP_A-1780278 BB 0.0408332
SNP_A-1780283 BB 0.00121666
SNP_A-1780290 AB 0.00224354
SNP_A-1780293 BB 0.00419706
SNP_A-1780299 AB 0.00368315
SNP_A-1780301 BB 0.024716
SNP_A-1780310 AA 0.0055109
SNP_A-1780315 AA 0.0265522
SNP_A-1780317 AB 0.00219966
SNP_A-1780319 BB 0.00209819
SNP_A-1780324 BB 0.0130823
SNP_A-1780325 AB 0.000657387
SNP_A-1780328 AA 0.0252649
SNP_A-1780333 AB 0.00563662
SNP_A-1780335 BB 0.0739639
SNP_A-1780339 BB 0.000204441
SNP_A-1780340 AA 0.0041103

Total number of rows: 238304

Table truncated, full table size 6348 Kbytes.




Supplementary file Size Download File type/resource
GSM1197269_HCC109N-Sty.CEL.gz 27.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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