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Sample GSM617753 Query DataSets for GSM617753
Status Public on Sep 01, 2011
Title OSCC tumor_OR4004
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 BB 293.45403 2098.99775
AFFX-SNP_10009702 AB 862.14622 575.35439
AFFX-SNP_10015773 AA 1840.72256 911.56223
AFFX-SNP_10021569 AA 752.96283 327.07743
AFFX-SNP_10026879 BB 624.87906 1866.18833
AFFX-SNP_10029725 BB 329.01795 521.63930
AFFX-SNP_10034687 AA 629.22055 341.83083
AFFX-SNP_10036267 AB 441.47928 500.51000
AFFX-SNP_10037362 BB 978.79250 3363.31420
AFFX-SNP_10037636 BB 220.95479 940.47665
AFFX-SNP_10039349 BB 265.36027 1001.17096
AFFX-SNP_10039442 AA 1533.98739 212.55501
AFFX-SNP_10039933 AB 1337.73117 1367.88319
AFFX-SNP_10046830 AB 972.35358 1025.88680
AFFX-SNP_10047363 AB 437.71310 377.08493
AFFX-SNP_10047841 AB 828.99745 804.71936
AFFX-SNP_10049334 AB 1913.49976 1265.23585
AFFX-SNP_10052664 BB 294.06265 1006.32517
AFFX-SNP_10057887 BB 242.20141 824.30590
AFFX-SNP_10064911 AA 737.32484 245.37186

Total number of rows: 909622

Table truncated, full table size 33725 Kbytes.

Supplementary file Size Download File type/resource
GSM617753_OR4004.CEL.gz 33.2 Mb (ftp)(http) CEL
GSM617753_OR4004.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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