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Sample GSM617705 Query DataSets for GSM617705
Status Public on Sep 01, 2011
Title OSCC tumor_OR2309
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 631.91307 1612.85632
AFFX-SNP_10009702 AA 998.70440 289.91204
AFFX-SNP_10015773 AA 1991.05430 1020.90949
AFFX-SNP_10021569 AA 815.41610 431.95084
AFFX-SNP_10026879 BB 653.05626 1947.80230
AFFX-SNP_10029725 AB 562.78095 505.23370
AFFX-SNP_10034687 AA 505.66127 411.02323
AFFX-SNP_10036267 AB 522.76379 580.23043
AFFX-SNP_10037362 BB 999.74155 3917.89253
AFFX-SNP_10037636 BB 193.52242 849.77500
AFFX-SNP_10039349 BB 331.75453 1384.33086
AFFX-SNP_10039442 AA 1399.67041 215.25188
AFFX-SNP_10039933 BB 756.17540 1967.07881
AFFX-SNP_10046830 AA 1592.40068 303.27504
AFFX-SNP_10047363 AB 507.37489 426.94615
AFFX-SNP_10047841 AB 717.25125 879.33761
AFFX-SNP_10049334 AB 1492.07124 1341.51107
AFFX-SNP_10052664 BB 278.86059 1138.53766
AFFX-SNP_10057887 AB 502.21634 697.31915
AFFX-SNP_10064911 AA 1030.02926 191.84593

Total number of rows: 909622

Table truncated, full table size 33779 Kbytes.

Supplementary file Size Download File type/resource
GSM617705_OR2309.CEL.gz 33.4 Mb (ftp)(http) CEL
GSM617705_OR2309.birdseed.chp.gz 13.2 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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