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Sample GSM617673 Query DataSets for GSM617673
Status Public on Sep 01, 2011
Title OSCC tumor_OR1019
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 986.52230 283.36271
AFFX-SNP_10009702 AB 677.53815 669.61308
AFFX-SNP_10015773 AA 1984.21942 1068.84637
AFFX-SNP_10021569 AA 822.42151 480.87258
AFFX-SNP_10026879 BB 591.69637 1982.89586
AFFX-SNP_10029725 AB 682.67612 508.93704
AFFX-SNP_10034687 AA 1173.88606 451.40921
AFFX-SNP_10036267 BB 400.69706 822.77206
AFFX-SNP_10037362 BB 988.61699 3505.07350
AFFX-SNP_10037636 BB 219.05934 828.74670
AFFX-SNP_10039349 BB 306.00947 1170.98685
AFFX-SNP_10039442 AA 1370.99218 193.08646
AFFX-SNP_10039933 BB 748.08381 1663.00159
AFFX-SNP_10046830 BB 249.22460 1779.39234
AFFX-SNP_10047363 BB 371.86112 740.66230
AFFX-SNP_10047841 AA 1383.40238 402.70142
AFFX-SNP_10049334 BB 535.38193 1811.07272
AFFX-SNP_10052664 BB 309.68505 1043.84420
AFFX-SNP_10057887 BB 251.18350 743.77369
AFFX-SNP_10064911 AB 796.20013 813.71345

Total number of rows: 909622

Table truncated, full table size 33759 Kbytes.

Supplementary file Size Download File type/resource
GSM617673_OR1019.CEL.gz 32.1 Mb (ftp)(http) CEL
GSM617673_OR1019.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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