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Sample GSM617676 Query DataSets for GSM617676
Status Public on Sep 01, 2011
Title OSCC tumor_OR1219
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 AB 715.41593 1647.92913
AFFX-SNP_10009702 AB 879.06959 640.95909
AFFX-SNP_10015773 AA 1960.18210 1040.81659
AFFX-SNP_10021569 AA 794.17102 424.46674
AFFX-SNP_10026879 BB 707.15981 1820.04628
AFFX-SNP_10029725 BB 339.02775 600.16356
AFFX-SNP_10034687 AA 1312.16903 545.65823
AFFX-SNP_10036267 BB 366.35395 703.58990
AFFX-SNP_10037362 BB 969.98846 3605.17402
AFFX-SNP_10037636 BB 234.81507 821.76646
AFFX-SNP_10039349 BB 261.60110 1192.49049
AFFX-SNP_10039442 AA 1591.32721 205.69309
AFFX-SNP_10039933 BB 687.50811 2070.09597
AFFX-SNP_10046830 BB 218.63115 1859.23814
AFFX-SNP_10047363 AB 533.97958 694.09984
AFFX-SNP_10047841 AB 854.27703 812.99326
AFFX-SNP_10049334 AB 1772.57180 1753.36066
AFFX-SNP_10052664 AB 569.44027 712.11504
AFFX-SNP_10057887 BB 315.92747 854.02587
AFFX-SNP_10064911 BB 366.18344 1035.97278

Total number of rows: 909622

Table truncated, full table size 33746 Kbytes.

Supplementary file Size Download File type/resource
GSM617676_OR1219.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM617676_OR1219.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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