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Sample GSM617686 Query DataSets for GSM617686
Status Public on Sep 01, 2011
Title OSCC tumor_OR1325
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 729.93027 1557.09620
AFFX-SNP_10009702 AA 1365.40317 284.47347
AFFX-SNP_10015773 AB 1703.32959 1920.85339
AFFX-SNP_10021569 AA 701.84816 313.91161
AFFX-SNP_10026879 BB 633.52855 1710.24904
AFFX-SNP_10029725 BB 373.55579 804.06539
AFFX-SNP_10034687 AA 1051.28972 358.16842
AFFX-SNP_10036267 BB 331.00870 722.40621
AFFX-SNP_10037362 BB 1024.53085 3534.71723
AFFX-SNP_10037636 BB 206.38786 874.20577
AFFX-SNP_10039349 AB 1035.76627 1009.60890
AFFX-SNP_10039442 AA 1639.22172 205.20225
AFFX-SNP_10039933 AB 1316.37755 1103.34267
AFFX-SNP_10046830 AA 1250.24069 255.62906
AFFX-SNP_10047363 BB 339.62046 828.91324
AFFX-SNP_10047841 BB 559.70899 1313.24621
AFFX-SNP_10049334 AA 2628.17512 464.88904
AFFX-SNP_10052664 BB 287.73667 914.91238
AFFX-SNP_10057887 AB 771.47011 602.80972
AFFX-SNP_10064911 AA 1081.09558 275.93216

Total number of rows: 909622

Table truncated, full table size 33739 Kbytes.

Supplementary file Size Download File type/resource
GSM617686_OR1325.CEL.gz 33.2 Mb (ftp)(http) CEL
GSM617686_OR1325.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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