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Sample GSM617776 Query DataSets for GSM617776
Status Public on Sep 01, 2011
Title Normal oral tissue_ON68
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 645.58953 1396.59617
AFFX-SNP_10009702 AB 853.04775 562.57274
AFFX-SNP_10015773 AB 1523.30829 1600.32006
AFFX-SNP_10021569 AA 735.40363 412.34077
AFFX-SNP_10026879 BB 643.40532 1707.69627
AFFX-SNP_10029725 BB 368.24656 614.16782
AFFX-SNP_10034687 AA 1166.40278 416.04015
AFFX-SNP_10036267 AB 462.48882 548.52837
AFFX-SNP_10037362 BB 906.79797 3766.78376
AFFX-SNP_10037636 BB 209.53853 905.11420
AFFX-SNP_10039349 AB 875.36428 639.75597
AFFX-SNP_10039442 AA 1544.93009 249.25467
AFFX-SNP_10039933 BB 650.67287 1866.75706
AFFX-SNP_10046830 BB 295.88270 1850.55790
AFFX-SNP_10047363 AB 611.00102 486.14864
AFFX-SNP_10047841 AA 1283.16969 360.77430
AFFX-SNP_10049334 BB 467.75628 1859.00797
AFFX-SNP_10052664 BB 304.36468 1112.52931
AFFX-SNP_10057887 BB 313.79022 872.26026
AFFX-SNP_10064911 AB 616.03553 593.33299

Total number of rows: 909622

Table truncated, full table size 33720 Kbytes.

Supplementary file Size Download File type/resource
GSM617776_ON68.CEL.gz 33.2 Mb (ftp)(http) CEL
GSM617776_ON68.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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