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Sample GSM617751 Query DataSets for GSM617751
Status Public on Sep 01, 2011
Title OSCC tumor_OR3407
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 757.72917 1701.33009
AFFX-SNP_10009702 AB 892.01662 750.15859
AFFX-SNP_10015773 AB 1537.89860 1481.36455
AFFX-SNP_10021569 AA 777.80778 291.16713
AFFX-SNP_10026879 BB 553.75691 1723.10493
AFFX-SNP_10029725 AB 479.16797 379.21246
AFFX-SNP_10034687 AA 918.71340 318.49064
AFFX-SNP_10036267 BB 295.69540 761.39332
AFFX-SNP_10037362 BB 907.29948 3429.48383
AFFX-SNP_10037636 BB 197.35619 897.81798
AFFX-SNP_10039349 BB 284.28399 1199.94572
AFFX-SNP_10039442 AA 1386.61037 222.93385
AFFX-SNP_10039933 BB 632.47573 1783.23232
AFFX-SNP_10046830 BB 280.75098 1813.28403
AFFX-SNP_10047363 BB 295.17906 793.73979
AFFX-SNP_10047841 AB 883.02311 749.73242
AFFX-SNP_10049334 AB 1455.38764 1229.73999
AFFX-SNP_10052664 BB 247.25949 926.63901
AFFX-SNP_10057887 AB 612.78110 540.62432
AFFX-SNP_10064911 AB 559.36127 657.28155

Total number of rows: 909622

Table truncated, full table size 33716 Kbytes.

Supplementary file Size Download File type/resource
GSM617751_OR3407.CEL.gz 34.0 Mb (ftp)(http) CEL
GSM617751_OR3407.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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