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Sample GSM617674 Query DataSets for GSM617674
Status Public on Sep 01, 2011
Title OSCC tumor_OR1058
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 1039.26716 230.36065
AFFX-SNP_10009702 AB 748.49906 518.41269
AFFX-SNP_10015773 AA 1963.47653 905.07308
AFFX-SNP_10021569 AA 674.39552 438.67988
AFFX-SNP_10026879 BB 576.72436 2128.87394
AFFX-SNP_10029725 BB 443.43432 590.57213
AFFX-SNP_10034687 AB 734.56429 880.87450
AFFX-SNP_10036267 BB 366.13607 817.97404
AFFX-SNP_10037362 BB 1038.76092 4212.48524
AFFX-SNP_10037636 BB 226.75444 844.86919
AFFX-SNP_10039349 AB 857.02976 722.78451
AFFX-SNP_10039442 AA 1594.00579 229.28277
AFFX-SNP_10039933 BB 684.18656 2015.49385
AFFX-SNP_10046830 AA 1475.48148 293.67241
AFFX-SNP_10047363 AB 488.93964 532.06468
AFFX-SNP_10047841 AB 995.65258 1035.87781
AFFX-SNP_10049334 BB 565.23146 1922.83536
AFFX-SNP_10052664 BB 298.21756 947.19235
AFFX-SNP_10057887 AB 486.11655 619.41558
AFFX-SNP_10064911 AB 876.65238 703.06339

Total number of rows: 909622

Table truncated, full table size 33730 Kbytes.

Supplementary file Size Download File type/resource
GSM617674_OR1058.CEL.gz 32.5 Mb (ftp)(http) CEL
GSM617674_OR1058.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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