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Sample GSM617768 Query DataSets for GSM617768
Status Public on Sep 01, 2011
Title OSCC tumor_OR4155
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 1212.50449 235.25729
AFFX-SNP_10009702 AA 1193.28779 260.10016
AFFX-SNP_10015773 AB 1381.88137 1380.84524
AFFX-SNP_10021569 AA 780.08379 450.72329
AFFX-SNP_10026879 BB 606.34943 1789.50913
AFFX-SNP_10029725 BB 351.84436 498.18263
AFFX-SNP_10034687 AB 811.04470 812.65494
AFFX-SNP_10036267 BB 305.74751 965.76418
AFFX-SNP_10037362 BB 909.25961 3537.64611
AFFX-SNP_10037636 BB 202.79929 848.44980
AFFX-SNP_10039349 BB 283.61806 998.99494
AFFX-SNP_10039442 AA 1450.12688 182.37600
AFFX-SNP_10039933 BB 610.45516 1775.10888
AFFX-SNP_10046830 BB 266.21611 1746.62113
AFFX-SNP_10047363 AB 528.28626 478.14921
AFFX-SNP_10047841 AB 982.41611 728.70194
AFFX-SNP_10049334 AB 1735.64245 1177.83305
AFFX-SNP_10052664 BB 286.72203 880.07168
AFFX-SNP_10057887 BB 285.19606 744.86192
AFFX-SNP_10064911 AB 726.69309 782.89691

Total number of rows: 909622

Table truncated, full table size 33733 Kbytes.

Supplementary file Size Download File type/resource
GSM617768_OR4155.CEL.gz 33.4 Mb (ftp)(http) CEL
GSM617768_OR4155.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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