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Sample GSM617767 Query DataSets for GSM617767
Status Public on Sep 01, 2011
Title OSCC tumor_OR4146
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 1168.10240 223.40103
AFFX-SNP_10009702 AA 1412.11129 274.00411
AFFX-SNP_10015773 AB 1678.54821 1288.14749
AFFX-SNP_10021569 AA 782.32276 454.97224
AFFX-SNP_10026879 BB 563.48060 1951.22415
AFFX-SNP_10029725 AB 547.86029 437.55527
AFFX-SNP_10034687 AB 781.31633 1010.08419
AFFX-SNP_10036267 BB 372.59877 799.89852
AFFX-SNP_10037362 AB 3810.02573 2638.79512
AFFX-SNP_10037636 BB 201.05467 833.33495
AFFX-SNP_10039349 BB 324.56094 1117.61896
AFFX-SNP_10039442 AA 1344.37118 187.79768
AFFX-SNP_10039933 BB 799.99575 2059.98979
AFFX-SNP_10046830 AB 734.35958 1145.63991
AFFX-SNP_10047363 AB 673.57518 442.64351
AFFX-SNP_10047841 AB 838.52367 796.42480
AFFX-SNP_10049334 AB 1863.84969 1713.22129
AFFX-SNP_10052664 BB 324.37426 1040.39154
AFFX-SNP_10057887 AB 412.82140 574.01822
AFFX-SNP_10064911 BB 500.92931 1243.09807

Total number of rows: 909622

Table truncated, full table size 33783 Kbytes.

Supplementary file Size Download File type/resource
GSM617767_OR4146.CEL.gz 33.6 Mb (ftp)(http) CEL
GSM617767_OR4146.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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