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Sample GSM617763 Query DataSets for GSM617763
Status Public on Sep 01, 2011
Title OSCC tumor_OR4087
Sample type genomic
Source name OSCC specimens
Organism Homo sapiens
Characteristics disease state: tumor
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 BB 302.60112 2562.00779
AFFX-SNP_10009702 AB 927.17998 659.16492
AFFX-SNP_10015773 AA 1727.06193 949.34872
AFFX-SNP_10021569 AA 795.73976 444.04960
AFFX-SNP_10026879 BB 641.59267 1863.24896
AFFX-SNP_10029725 AB 470.35826 465.37821
AFFX-SNP_10034687 AA 668.72888 434.96992
AFFX-SNP_10036267 BB 315.55769 840.81771
AFFX-SNP_10037362 BB 844.39227 3861.41621
AFFX-SNP_10037636 BB 223.51167 1035.89806
AFFX-SNP_10039349 AB 840.48587 802.39465
AFFX-SNP_10039442 AA 1320.41794 198.35466
AFFX-SNP_10039933 BB 706.94889 2012.16419
AFFX-SNP_10046830 BB 236.83797 1614.52543
AFFX-SNP_10047363 AB 490.80761 507.72734
AFFX-SNP_10047841 AB 751.52735 797.51203
AFFX-SNP_10049334 AA 2984.52494 453.54715
AFFX-SNP_10052664 BB 273.64104 969.44507
AFFX-SNP_10057887 AA 854.62354 312.36267
AFFX-SNP_10064911 AA 796.28500 297.71798

Total number of rows: 909622

Table truncated, full table size 33727 Kbytes.

Supplementary file Size Download File type/resource
GSM617763_OR4087.CEL.gz 32.8 Mb (ftp)(http) CEL
GSM617763_OR4087.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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