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Sample GSM617780 Query DataSets for GSM617780
Status Public on Sep 01, 2011
Title Normal oral tissue_ON81
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 1033.10891 198.33189
AFFX-SNP_10009702 AB 878.93371 592.79919
AFFX-SNP_10015773 AA 1704.79056 796.82206
AFFX-SNP_10021569 AA 749.53850 394.65353
AFFX-SNP_10026879 BB 590.50962 1719.63679
AFFX-SNP_10029725 BB 325.92512 547.38825
AFFX-SNP_10034687 AA 1021.04179 381.75992
AFFX-SNP_10036267 BB 350.36773 829.38307
AFFX-SNP_10037362 AB 2545.07940 2530.77949
AFFX-SNP_10037636 BB 212.91088 882.89451
AFFX-SNP_10039349 BB 285.92981 1137.35229
AFFX-SNP_10039442 AA 1425.36025 221.68412
AFFX-SNP_10039933 BB 696.04551 1948.65874
AFFX-SNP_10046830 BB 295.45749 1719.70866
AFFX-SNP_10047363 BB 359.83213 727.86006
AFFX-SNP_10047841 AB 732.00329 984.07278
AFFX-SNP_10049334 AA 2828.10651 465.09733
AFFX-SNP_10052664 BB 260.82617 1034.54308
AFFX-SNP_10057887 AB 609.81864 688.10238
AFFX-SNP_10064911 AB 653.40611 670.56001

Total number of rows: 909622

Table truncated, full table size 33719 Kbytes.

Supplementary file Size Download File type/resource
GSM617780_ON81.CEL.gz 33.7 Mb (ftp)(http) CEL
GSM617780_ON81.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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