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Sample GSM617758 Query DataSets for GSM617758
Status Public on Sep 01, 2011
Title OSCC tumor_OR4052
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 915.57877 250.67523
AFFX-SNP_10009702 AA 1247.56688 327.87085
AFFX-SNP_10015773 AA 1765.73058 1039.92055
AFFX-SNP_10021569 AA 612.61170 417.42143
AFFX-SNP_10026879 BB 669.67168 1817.81943
AFFX-SNP_10029725 AB 556.01370 490.69741
AFFX-SNP_10034687 AA 777.96680 422.65785
AFFX-SNP_10036267 BB 365.00125 771.50204
AFFX-SNP_10037362 BB 1020.91915 3736.27103
AFFX-SNP_10037636 BB 214.23358 790.08873
AFFX-SNP_10039349 AB 692.88584 520.46711
AFFX-SNP_10039442 AA 1415.79879 207.10461
AFFX-SNP_10039933 BB 930.24557 2191.37868
AFFX-SNP_10046830 AB 798.51735 1084.41552
AFFX-SNP_10047363 BB 440.60849 697.24393
AFFX-SNP_10047841 AB 1062.52313 786.15835
AFFX-SNP_10049334 BB 404.46707 1992.14528
AFFX-SNP_10052664 BB 253.57577 837.14389
AFFX-SNP_10057887 AB 601.63726 663.96353
AFFX-SNP_10064911 AB 809.70028 613.47418

Total number of rows: 909622

Table truncated, full table size 33732 Kbytes.

Supplementary file Size Download File type/resource
GSM617758_OR4052.CEL.gz 32.5 Mb (ftp)(http) CEL
GSM617758_OR4052.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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