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Sample GSM617663 Query DataSets for GSM617663
Status Public on Sep 01, 2011
Title OSCC tumor_OR0816
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 721.71829 1130.45449
AFFX-SNP_10009702 AA 1125.68659 251.46069
AFFX-SNP_10015773 AB 1612.13726 1607.06756
AFFX-SNP_10021569 AA 692.58996 364.31720
AFFX-SNP_10026879 AB 1519.65815 1545.80211
AFFX-SNP_10029725 AB 594.45104 577.99260
AFFX-SNP_10034687 AA 849.69156 454.82888
AFFX-SNP_10036267 AB 439.16744 529.17191
AFFX-SNP_10037362 BB 1083.15793 3901.16497
AFFX-SNP_10037636 BB 241.30156 879.80312
AFFX-SNP_10039349 AB 751.24988 586.27675
AFFX-SNP_10039442 AA 1303.40813 225.05655
AFFX-SNP_10039933 AB 1710.39541 1222.56292
AFFX-SNP_10046830 AB 779.96401 1223.74621
AFFX-SNP_10047363 AB 482.63666 442.28818
AFFX-SNP_10047841 BB 796.78066 1206.13090
AFFX-SNP_10049334 AA 2850.34505 529.80844
AFFX-SNP_10052664 BB 298.03144 903.23054
AFFX-SNP_10057887 AB 531.56389 646.05491
AFFX-SNP_10064911 AB 660.30537 649.72042

Total number of rows: 909622

Table truncated, full table size 33739 Kbytes.

Supplementary file Size Download File type/resource
GSM617663_OR0816.CEL.gz 31.9 Mb (ftp)(http) CEL
GSM617663_OR0816.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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