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Sample GSM617704 Query DataSets for GSM617704
Status Public on Sep 01, 2011
Title OSCC tumor_OR2267
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 NoCall 1162.60927 1435.94303
AFFX-SNP_10009702 BB 356.40043 664.23563
AFFX-SNP_10015773 AA 2106.51353 1273.33106
AFFX-SNP_10021569 AA 955.87943 539.10041
AFFX-SNP_10026879 BB 694.14710 1987.93593
AFFX-SNP_10029725 BB 420.03569 539.98078
AFFX-SNP_10034687 AA 1017.19511 517.79793
AFFX-SNP_10036267 BB 348.46871 821.58900
AFFX-SNP_10037362 BB 1046.09787 3260.13288
AFFX-SNP_10037636 BB 189.45995 886.96474
AFFX-SNP_10039349 AB 908.78707 780.36283
AFFX-SNP_10039442 AA 1446.55570 171.12646
AFFX-SNP_10039933 BB 834.69391 1946.14065
AFFX-SNP_10046830 AA 1070.75365 536.81442
AFFX-SNP_10047363 AA 727.30542 287.04429
AFFX-SNP_10047841 AB 1004.45175 726.38966
AFFX-SNP_10049334 AA 2980.80098 686.46312
AFFX-SNP_10052664 BB 305.92984 814.60314
AFFX-SNP_10057887 AB 421.37037 521.25347
AFFX-SNP_10064911 AB 900.16071 624.03576

Total number of rows: 909622

Table truncated, full table size 33787 Kbytes.

Supplementary file Size Download File type/resource
GSM617704_OR2267.CEL.gz 31.4 Mb (ftp)(http) CEL
GSM617704_OR2267.birdseed.chp.gz 13.0 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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