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Sample GSM617717 Query DataSets for GSM617717
Status Public on Sep 01, 2011
Title OSCC tumor_OR2451
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 742.22854 1399.06251
AFFX-SNP_10009702 AB 849.08693 570.62932
AFFX-SNP_10015773 AA 1752.23941 956.44537
AFFX-SNP_10021569 AA 752.21168 365.90176
AFFX-SNP_10026879 AB 2297.30315 1385.25297
AFFX-SNP_10029725 AB 526.22694 426.42180
AFFX-SNP_10034687 AA 738.14132 401.36222
AFFX-SNP_10036267 BB 298.48606 824.71643
AFFX-SNP_10037362 BB 1043.99396 3513.15619
AFFX-SNP_10037636 BB 217.22343 753.72985
AFFX-SNP_10039349 BB 286.92001 1214.95553
AFFX-SNP_10039442 AA 1333.77370 211.26366
AFFX-SNP_10039933 BB 811.19527 1976.41006
AFFX-SNP_10046830 AB 960.31333 1123.45402
AFFX-SNP_10047363 AB 622.70147 467.01556
AFFX-SNP_10047841 BB 642.38163 1390.64015
AFFX-SNP_10049334 BB 400.64818 2080.53936
AFFX-SNP_10052664 BB 283.02732 1077.74404
AFFX-SNP_10057887 AB 566.47492 564.35921
AFFX-SNP_10064911 BB 516.09142 1231.70035

Total number of rows: 909622

Table truncated, full table size 33768 Kbytes.

Supplementary file Size Download File type/resource
GSM617717_OR2451.CEL.gz 34.2 Mb (ftp)(http) CEL
GSM617717_OR2451.birdseed.chp.gz 13.2 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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