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Sample GSM617666 Query DataSets for GSM617666
Status Public on Sep 01, 2011
Title OSCC tumor_OR0936
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 AB 764.73701 1507.06515
AFFX-SNP_10009702 AB 566.73223 442.44839
AFFX-SNP_10015773 AA 1866.16574 1073.99060
AFFX-SNP_10021569 AA 711.56541 411.07558
AFFX-SNP_10026879 BB 661.75432 1880.05917
AFFX-SNP_10029725 BB 467.79567 586.39185
AFFX-SNP_10034687 AA 582.07275 464.11861
AFFX-SNP_10036267 AA 615.67048 332.45333
AFFX-SNP_10037362 BB 967.80432 3914.30538
AFFX-SNP_10037636 BB 254.67940 714.85059
AFFX-SNP_10039349 BB 295.73654 1212.47733
AFFX-SNP_10039442 AA 1936.06193 201.80839
AFFX-SNP_10039933 BB 803.83218 1502.50224
AFFX-SNP_10046830 AA 1346.98844 323.20175
AFFX-SNP_10047363 AA 722.31048 271.57552
AFFX-SNP_10047841 BB 644.80194 1179.46525
AFFX-SNP_10049334 BB 407.44129 1679.25454
AFFX-SNP_10052664 BB 327.57371 1054.48073
AFFX-SNP_10057887 AB 619.31442 617.68493
AFFX-SNP_10064911 AB 967.77091 1219.19227

Total number of rows: 909622

Table truncated, full table size 33782 Kbytes.

Supplementary file Size Download File type/resource
GSM617666_OR0936.CEL.gz 31.8 Mb (ftp)(http) CEL
GSM617666_OR0936.birdseed.chp.gz 13.0 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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