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Sample GSM617700 Query DataSets for GSM617700
Status Public on Sep 01, 2011
Title OSCC tumor_OR2193
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 1053.07226 219.39626
AFFX-SNP_10009702 AB 653.65875 676.96895
AFFX-SNP_10015773 AA 1825.97827 1063.60993
AFFX-SNP_10021569 AA 695.79550 478.96891
AFFX-SNP_10026879 AA 2379.99666 666.25921
AFFX-SNP_10029725 AA 701.52760 354.53598
AFFX-SNP_10034687 AB 639.35012 926.27770
AFFX-SNP_10036267 AB 447.89907 567.86559
AFFX-SNP_10037362 BB 1054.43062 3408.28732
AFFX-SNP_10037636 BB 194.07647 909.11790
AFFX-SNP_10039349 BB 259.60338 835.71578
AFFX-SNP_10039442 AA 1208.49812 183.98067
AFFX-SNP_10039933 BB 816.61212 1851.05551
AFFX-SNP_10046830 BB 239.00610 2091.04225
AFFX-SNP_10047363 BB 312.53608 651.17797
AFFX-SNP_10047841 AB 1092.42859 827.14169
AFFX-SNP_10049334 AB 1898.89545 1534.56713
AFFX-SNP_10052664 AB 464.78073 677.59266
AFFX-SNP_10057887 AA 840.53474 368.34243
AFFX-SNP_10064911 AB 737.50557 864.98883

Total number of rows: 909622

Table truncated, full table size 33746 Kbytes.

Supplementary file Size Download File type/resource
GSM617700_OR2193.CEL.gz 32.4 Mb (ftp)(http) CEL
GSM617700_OR2193.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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