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Sample GSM617754 Query DataSets for GSM617754
Status Public on Sep 01, 2011
Title OSCC tumor_OR4015
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 1094.63427 186.43360
AFFX-SNP_10009702 BB 353.79079 949.33158
AFFX-SNP_10015773 BB 1271.68373 1998.84619
AFFX-SNP_10021569 AA 819.87403 434.45927
AFFX-SNP_10026879 AB 1419.79222 1642.56388
AFFX-SNP_10029725 NoCall 462.40185 504.41561
AFFX-SNP_10034687 AA 1402.94015 412.40070
AFFX-SNP_10036267 AB 399.93488 561.38652
AFFX-SNP_10037362 BB 915.34142 3481.73217
AFFX-SNP_10037636 BB 231.11526 900.62772
AFFX-SNP_10039349 NoCall 639.12745 1119.52127
AFFX-SNP_10039442 AA 1560.21026 214.10040
AFFX-SNP_10039933 AB 1335.98847 1179.26497
AFFX-SNP_10046830 BB 332.76046 1925.68398
AFFX-SNP_10047363 AA 747.24550 217.78199
AFFX-SNP_10047841 BB 602.03334 1304.57166
AFFX-SNP_10049334 AA 2783.40902 505.64309
AFFX-SNP_10052664 BB 288.14808 1096.32148
AFFX-SNP_10057887 BB 297.72469 838.46197
AFFX-SNP_10064911 AA 884.15014 292.00391

Total number of rows: 909622

Table truncated, full table size 33754 Kbytes.

Supplementary file Size Download File type/resource
GSM617754_OR4015.CEL.gz 32.6 Mb (ftp)(http) CEL
GSM617754_OR4015.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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