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Sample GSM617684 Query DataSets for GSM617684
Status Public on Sep 01, 2011
Title OSCC tumor_OR1293
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 1179.03078 235.23304
AFFX-SNP_10009702 AB 919.19259 461.84728
AFFX-SNP_10015773 AA 2002.86098 970.43903
AFFX-SNP_10021569 AA 688.96760 387.64307
AFFX-SNP_10026879 AA 1884.29184 707.54868
AFFX-SNP_10029725 AA 992.88945 356.25184
AFFX-SNP_10034687 AB 503.64554 809.99640
AFFX-SNP_10036267 BB 531.13498 828.49177
AFFX-SNP_10037362 BB 1016.07800 3405.12320
AFFX-SNP_10037636 BB 225.83234 747.23421
AFFX-SNP_10039349 BB 335.42485 1216.27363
AFFX-SNP_10039442 AA 1570.17246 200.29499
AFFX-SNP_10039933 BB 723.98159 2027.32653
AFFX-SNP_10046830 BB 269.93467 1810.67372
AFFX-SNP_10047363 BB 361.21732 744.29504
AFFX-SNP_10047841 AB 982.86240 815.42221
AFFX-SNP_10049334 AB 1139.85683 1535.49450
AFFX-SNP_10052664 AB 613.83886 630.23206
AFFX-SNP_10057887 AA 762.82812 372.72084
AFFX-SNP_10064911 AB 971.22341 813.63352

Total number of rows: 909622

Table truncated, full table size 33767 Kbytes.

Supplementary file Size Download File type/resource
GSM617684_OR1293.CEL.gz 32.9 Mb (ftp)(http) CEL
GSM617684_OR1293.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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