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Sample GSM617703 Query DataSets for GSM617703
Status Public on Sep 01, 2011
Title OSCC tumor_OR2266
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 AA 970.95067 184.50722
AFFX-SNP_10009702 AA 1239.29054 274.48020
AFFX-SNP_10015773 BB 1358.34930 2258.70511
AFFX-SNP_10021569 AA 718.35346 371.61462
AFFX-SNP_10026879 AB 1353.62597 1449.00815
AFFX-SNP_10029725 AB 501.82486 444.35944
AFFX-SNP_10034687 AA 886.80443 392.63008
AFFX-SNP_10036267 BB 322.07577 669.90001
AFFX-SNP_10037362 BB 1111.60843 4418.40235
AFFX-SNP_10037636 BB 179.30384 881.31579
AFFX-SNP_10039349 BB 303.20187 1045.78479
AFFX-SNP_10039442 AA 1409.57524 232.19500
AFFX-SNP_10039933 BB 691.39954 2032.82710
AFFX-SNP_10046830 AA 1394.65376 300.69088
AFFX-SNP_10047363 AB 586.83449 474.25604
AFFX-SNP_10047841 AA 1116.85011 341.11288
AFFX-SNP_10049334 AB 1688.27772 1752.76005
AFFX-SNP_10052664 AB 656.56559 648.95547
AFFX-SNP_10057887 AB 493.60222 686.86262
AFFX-SNP_10064911 AA 1051.32345 244.08731

Total number of rows: 909622

Table truncated, full table size 33728 Kbytes.

Supplementary file Size Download File type/resource
GSM617703_OR2266.CEL.gz 33.5 Mb (ftp)(http) CEL
GSM617703_OR2266.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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