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Sample GSM617713 Query DataSets for GSM617713
Status Public on Sep 01, 2011
Title OSCC tumor_OR2403
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 AA 1071.10833 239.95038
AFFX-SNP_10009702 AB 967.43819 615.76297
AFFX-SNP_10015773 AA 1763.97443 1176.15209
AFFX-SNP_10021569 AA 785.55131 376.89119
AFFX-SNP_10026879 BB 731.26412 2127.15520
AFFX-SNP_10029725 BB 351.31214 710.68161
AFFX-SNP_10034687 AB 902.21968 829.32865
AFFX-SNP_10036267 BB 388.98384 772.35111
AFFX-SNP_10037362 BB 859.16029 3651.44448
AFFX-SNP_10037636 BB 261.89232 955.03973
AFFX-SNP_10039349 AB 819.96113 578.08245
AFFX-SNP_10039442 AA 1463.20363 225.20600
AFFX-SNP_10039933 BB 752.04716 1911.03020
AFFX-SNP_10046830 AA 1350.60598 289.58715
AFFX-SNP_10047363 AB 568.75827 525.96014
AFFX-SNP_10047841 AB 860.48526 785.25394
AFFX-SNP_10049334 BB 581.84014 2117.50963
AFFX-SNP_10052664 BB 300.75339 935.92717
AFFX-SNP_10057887 AB 584.47000 587.09074
AFFX-SNP_10064911 AB 713.80656 649.16192

Total number of rows: 909622

Table truncated, full table size 33726 Kbytes.

Supplementary file Size Download File type/resource
GSM617713_OR2403.CEL.gz 31.7 Mb (ftp)(http) CEL
GSM617713_OR2403.birdseed.chp.gz 13.0 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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