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Sample GSM617781 Query DataSets for GSM617781
Status Public on Sep 01, 2011
Title Normal oral tissue_ON82
Sample type genomic
Source name Normal oral tissue
Organism Homo sapiens
Characteristics disease state: norml
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 1027.92804 242.94490
AFFX-SNP_10009702 AA 1278.72539 263.59728
AFFX-SNP_10015773 AA 1761.02864 1002.67251
AFFX-SNP_10021569 AA 785.01303 475.09569
AFFX-SNP_10026879 AB 1509.00046 1481.20923
AFFX-SNP_10029725 AB 527.87773 391.91667
AFFX-SNP_10034687 BB 405.59823 1385.79770
AFFX-SNP_10036267 AB 426.45709 587.90293
AFFX-SNP_10037362 BB 915.29986 3703.10331
AFFX-SNP_10037636 BB 216.33446 875.06713
AFFX-SNP_10039349 BB 357.52052 1046.99597
AFFX-SNP_10039442 AA 1257.60674 221.76304
AFFX-SNP_10039933 BB 725.15726 2017.30823
AFFX-SNP_10046830 AB 929.28869 1055.55890
AFFX-SNP_10047363 AB 547.59822 539.99861
AFFX-SNP_10047841 AB 754.42073 921.36616
AFFX-SNP_10049334 AB 1956.90031 1299.79058
AFFX-SNP_10052664 BB 306.62335 1158.15968
AFFX-SNP_10057887 AB 552.41177 579.88174
AFFX-SNP_10064911 AB 674.71131 731.99124

Total number of rows: 909622

Table truncated, full table size 33727 Kbytes.

Supplementary file Size Download File type/resource
GSM617781_ON82.CEL.gz 31.9 Mb (ftp)(http) CEL
GSM617781_ON82.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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