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Sample GSM617775 Query DataSets for GSM617775
Status Public on Sep 01, 2011
Title Normal oral tissue_ON66
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 672.96160 1248.48262
AFFX-SNP_10009702 AB 822.47763 594.78898
AFFX-SNP_10015773 AB 1445.70356 1441.24899
AFFX-SNP_10021569 AA 704.17740 330.22595
AFFX-SNP_10026879 AB 1363.62812 1154.49908
AFFX-SNP_10029725 BB 357.21617 542.19843
AFFX-SNP_10034687 AA 803.63456 454.92612
AFFX-SNP_10036267 BB 303.44123 768.62622
AFFX-SNP_10037362 BB 1009.42240 3722.47541
AFFX-SNP_10037636 BB 215.75428 939.09651
AFFX-SNP_10039349 BB 277.81931 995.38153
AFFX-SNP_10039442 AA 1481.29080 183.27799
AFFX-SNP_10039933 BB 671.98066 1907.92759
AFFX-SNP_10046830 AB 784.22416 1082.45121
AFFX-SNP_10047363 BB 317.40711 641.61524
AFFX-SNP_10047841 AA 1290.11838 383.11523
AFFX-SNP_10049334 AB 1646.68597 1280.57717
AFFX-SNP_10052664 BB 244.48787 947.66119
AFFX-SNP_10057887 AB 588.14937 627.65121
AFFX-SNP_10064911 AB 641.36263 593.56255

Total number of rows: 909622

Table truncated, full table size 33719 Kbytes.

Supplementary file Size Download File type/resource
GSM617775_ON66.CEL.gz 33.3 Mb (ftp)(http) CEL
GSM617775_ON66.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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