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Sample GSM770039 Query DataSets for GSM770039
Status Public on Feb 10, 2012
Title Gastric primary tumor sample 006LTE SNP6
Sample type genomic
 
Source name Gastric primary tumor sample 006LTE
Organism Homo sapiens
Characteristics tissue: Gastric primary tumor 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 01, 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 0.551346 2.581229 nan nan
CN_473964 2.000000 1 51659 -0.143487 2.581153 nan nan
CN_473965 2.000000 1 51674 -0.198247 2.581137 nan nan
CN_473981 2.000000 1 52771 0.277408 2.579998 nan nan
CN_473982 2.000000 1 52788 0.637587 2.579980 nan nan
CN_497981 2.000000 1 62627 1.023503 2.569903 nan nan
CN_502615 2.000000 1 75787 -0.439836 2.556993 nan nan
CN_502613 2.000000 1 75849 0.198226 2.556934 nan nan
CN_502614 2.000000 1 76175 -0.003280 2.556625 nan nan
CN_502616 2.000000 1 76192 -0.342152 2.556609 nan nan
CN_502843 2.000000 1 88453 0.659412 2.545460 nan nan
CN_466171 2.000000 1 218557 -0.220365 2.758334 nan nan
CN_468414 2.000000 1 218926 0.570326 2.758376 nan nan
CN_468412 2.000000 1 219009 -0.015431 2.758386 nan nan
CN_468413 2.000000 1 219024 0.432760 2.758388 nan nan
CN_470565 2.000000 1 219470 0.477841 2.758438 nan nan
CN_468424 2.000000 1 225521 0.325082 2.759128 nan nan
CN_468425 2.000000 1 225579 0.234768 2.759134 nan nan
CN_460512 2.000000 1 346294 0.348027 1.855513 nan nan
CN_460513 2.000000 1 346393 -0.468287 1.855511 nan nan

Total number of rows: 1813441

Table truncated, full table size 114059 Kbytes.




Supplementary file Size Download File type/resource
GSM770039_GC-006LTE_V6.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM770039_GC-006LTE_V6.def.CN5.CNCHP.gz 34.7 Mb (ftp)(http) CNCHP
Processed data included within Sample table
Processed data provided as supplementary file

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