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Sample GSM617774 Query DataSets for GSM617774
Status Public on Sep 01, 2011
Title Normal oral tissue_ON64
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 AB 686.70373 1491.32211
AFFX-SNP_10009702 AA 1182.03422 310.28103
AFFX-SNP_10015773 AA 1981.67671 884.21246
AFFX-SNP_10021569 AA 744.12027 344.94227
AFFX-SNP_10026879 BB 525.95384 1826.37068
AFFX-SNP_10029725 BB 285.80087 571.71596
AFFX-SNP_10034687 AA 1318.83384 391.30005
AFFX-SNP_10036267 BB 385.29324 767.21880
AFFX-SNP_10037362 BB 864.45793 3894.04669
AFFX-SNP_10037636 BB 196.98049 1049.31727
AFFX-SNP_10039349 AA 1217.52901 289.99014
AFFX-SNP_10039442 AA 1567.96916 191.35120
AFFX-SNP_10039933 BB 675.68946 2090.06022
AFFX-SNP_10046830 AB 963.59132 1108.70001
AFFX-SNP_10047363 AB 533.07759 517.98819
AFFX-SNP_10047841 BB 549.08441 1310.22704
AFFX-SNP_10049334 AA 2926.18291 481.89225
AFFX-SNP_10052664 BB 312.76072 1046.17100
AFFX-SNP_10057887 BB 275.88920 788.64926
AFFX-SNP_10064911 AA 795.86922 261.98270

Total number of rows: 909622

Table truncated, full table size 33719 Kbytes.

Supplementary file Size Download File type/resource
GSM617774_ON64.CEL.gz 33.3 Mb (ftp)(http) CEL
GSM617774_ON64.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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