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Sample GSM617709 Query DataSets for GSM617709
Status Public on Sep 01, 2011
Title OSCC tumor_OR2343
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 AB 596.05103 1580.91078
AFFX-SNP_10009702 AA 1314.52337 296.18455
AFFX-SNP_10015773 AA 1798.19833 1008.61741
AFFX-SNP_10021569 AA 799.71386 473.84912
AFFX-SNP_10026879 BB 544.01913 2069.59088
AFFX-SNP_10029725 BB 420.22655 747.96774
AFFX-SNP_10034687 AB 534.77165 940.85865
AFFX-SNP_10036267 BB 360.70924 779.98136
AFFX-SNP_10037362 BB 938.15027 3707.68663
AFFX-SNP_10037636 BB 298.02377 863.23862
AFFX-SNP_10039349 BB 255.57710 954.62545
AFFX-SNP_10039442 AA 1428.52506 188.45133
AFFX-SNP_10039933 BB 731.97397 1770.25328
AFFX-SNP_10046830 AB 901.53415 1141.57401
AFFX-SNP_10047363 BB 275.22811 688.95059
AFFX-SNP_10047841 AA 1071.38762 428.01328
AFFX-SNP_10049334 AB 1848.26183 1347.19314
AFFX-SNP_10052664 AB 530.71066 735.04265
AFFX-SNP_10057887 AB 557.03984 592.03134
AFFX-SNP_10064911 AB 748.49333 597.16305

Total number of rows: 909622

Table truncated, full table size 33722 Kbytes.

Supplementary file Size Download File type/resource
GSM617709_OR2343.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM617709_OR2343.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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