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Sample GSM771149 Query DataSets for GSM771149
Status Public on Feb 10, 2012
Title Gastric primary non-malignant sample 990097N SNP6
Sample type genomic
 
Source name Gastric primary non-malignant sample 990097N
Organism Homo sapiens
Characteristics tissue: Gastric primary non-malignant tissue
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from flash-frozen gastric tumors and matched non-maligant gastric tissues using a Qiagen genomic DNA extraction kit.
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 SNP6 array
Data processing Analysis of raw cel files was performed by Affymetrix Genotyping Console 4.0 software. A reference Model File was created based on 98 non-malignant samples (included as Gastric Normal.REF in the submission). Gastric non-malignant samples and tumors samples were then processed separately using this referenece file by median normalization and GC correlation to obtain the CHP files.
 
Submission date Aug 02, 2011
Last update date Feb 10, 2012
Contact name Niantao Deng
Organization name Duke NUS Graduate Medical School
Street address Center for Computational Biology, level 6, 8 College Road
City Singapore
State/province Singapore
ZIP/Postal code 169857
Country Singapore
 
Platform ID GPL6801
Series (1)
GSE31168 Genetic Landscape of Copy Number Alterations in Gastric Cancer

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 2.000000 1 51586 -0.307689 1.860581 nan nan
CN_473964 2.000000 1 51659 -0.164854 1.860589 nan nan
CN_473965 2.000000 1 51674 0.210254 1.860591 nan nan
CN_473981 2.000000 1 52771 -0.170028 1.860716 nan nan
CN_473982 2.000000 1 52788 0.020190 1.860718 nan nan
CN_497981 2.000000 1 62627 0.008044 1.861767 nan nan
CN_502615 2.000000 1 75787 0.017899 1.862930 nan nan
CN_502613 2.000000 1 75849 0.210856 1.862934 nan nan
CN_502614 2.000000 1 76175 -0.100184 1.862959 nan nan
CN_502616 2.000000 1 76192 -0.229191 1.862961 nan nan
CN_502843 2.000000 1 88453 -0.135695 1.863761 nan nan
CN_466171 2.000000 1 218557 0.337539 2.603657 nan nan
CN_468414 2.000000 1 218926 0.347893 2.603477 nan nan
CN_468412 2.000000 1 219009 0.735796 2.603436 nan nan
CN_468413 2.000000 1 219024 0.209573 2.603429 nan nan
CN_470565 2.000000 1 219470 -0.212679 2.603211 nan nan
CN_468424 2.000000 1 225521 0.164580 2.600241 nan nan
CN_468425 2.000000 1 225579 -0.105732 2.600212 nan nan
CN_460512 2.000000 1 346294 -0.155308 1.693987 nan nan
CN_460513 2.000000 1 346393 -0.111016 1.693987 nan nan

Total number of rows: 1813441

Table truncated, full table size 114193 Kbytes.




Supplementary file Size Download File type/resource
GSM771149_GN-990097N_V6.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM771149_GN-990097N_V6.def.CN5.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file

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