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Sample GSM617719 Query DataSets for GSM617719
Status Public on Sep 01, 2011
Title OSCC tumor_OR2470
Sample type genomic
Source name OSCC specimens
Organism Homo sapiens
Characteristics disease state: tumor
Growth protocol Cell lines were grown according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen 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 Affymetrix SNP6.0
Data processing We used Partek to detect copy number variation. We used birdseed algorithm for calling SNP 6.0, which is suggested standard algorithm, and birdseed is embedded in software of Genotyping Console (GTC) or Affymetrix Power Tool (APT) which all provide by affymetrix company. The reported summarized intensity are separated into A intensity and B intensity, and results in calling into AA, AB, or BB categories.
Submission date Nov 04, 2010
Last update date Sep 01, 2011
Contact name Chien-Hua Peng
Organization name Chang Gung Memorial Hospital
Street address No. 5, Fu-Hsing ST.
City Taoyuan
ZIP/Postal code 33305
Country Taiwan
Platform ID GPL6801
Series (2)
GSE25103 Affymetrix SNP array data for oral squamous cell carcinoma
GSE25104 Expression and SNP array data for oral squamous cell carcinoma

Data table header descriptions
VALUE genotype call

Data table
ID_REF VALUE signalA signalB
AFFX-SNP_10000979 BB 285.44522 2611.24575
AFFX-SNP_10009702 AA 1268.34926 297.28564
AFFX-SNP_10015773 AA 1908.65241 1114.70860
AFFX-SNP_10021569 AA 790.33787 380.96346
AFFX-SNP_10026879 BB 587.89700 1888.30538
AFFX-SNP_10029725 AB 465.00045 499.67994
AFFX-SNP_10034687 AB 702.74661 829.20865
AFFX-SNP_10036267 AB 505.05379 471.86222
AFFX-SNP_10037362 BB 1195.14347 3675.59992
AFFX-SNP_10037636 BB 202.25215 880.46079
AFFX-SNP_10039349 BB 276.05439 930.15220
AFFX-SNP_10039442 AA 1350.95248 194.35854
AFFX-SNP_10039933 BB 889.16740 2126.16285
AFFX-SNP_10046830 AB 768.96884 1354.94053
AFFX-SNP_10047363 AB 621.08951 482.44370
AFFX-SNP_10047841 AA 1087.55631 377.22309
AFFX-SNP_10049334 AB 1749.77891 1361.42059
AFFX-SNP_10052664 BB 317.03976 810.11966
AFFX-SNP_10057887 AB 465.72140 571.81114
AFFX-SNP_10064911 AA 1000.13999 265.58488

Total number of rows: 909622

Table truncated, full table size 33770 Kbytes.

Supplementary file Size Download File type/resource
GSM617719_OR2470.CEL.gz 33.1 Mb (ftp)(http) CEL
GSM617719_OR2470.birdseed.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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