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Sample GSM617680 Query DataSets for GSM617680
Status Public on Sep 01, 2011
Title OSCC tumor_OR1272
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 704.16704 1571.38328
AFFX-SNP_10009702 AB 870.87858 744.12354
AFFX-SNP_10015773 AB 1610.80046 1603.44000
AFFX-SNP_10021569 AA 716.18393 342.42175
AFFX-SNP_10026879 BB 615.51433 1876.90526
AFFX-SNP_10029725 AA 794.82468 346.86865
AFFX-SNP_10034687 AA 884.81412 380.37853
AFFX-SNP_10036267 AB 471.72000 625.65571
AFFX-SNP_10037362 BB 1029.27291 3816.61995
AFFX-SNP_10037636 BB 238.67126 871.08738
AFFX-SNP_10039349 BB 248.58693 1035.88398
AFFX-SNP_10039442 AA 1536.20610 234.80186
AFFX-SNP_10039933 AB 1413.99437 1405.72815
AFFX-SNP_10046830 AA 1356.20602 340.77448
AFFX-SNP_10047363 BB 295.88061 759.47802
AFFX-SNP_10047841 AB 946.11108 885.51367
AFFX-SNP_10049334 AB 1850.08933 1217.20303
AFFX-SNP_10052664 BB 279.28519 932.17750
AFFX-SNP_10057887 BB 277.56410 834.10239
AFFX-SNP_10064911 AB 712.20493 756.06743

Total number of rows: 909622

Table truncated, full table size 33721 Kbytes.

Supplementary file Size Download File type/resource
GSM617680_OR1272.CEL.gz 33.3 Mb (ftp)(http) CEL
GSM617680_OR1272.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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