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Sample GSM617683 Query DataSets for GSM617683
Status Public on Sep 01, 2011
Title OSCC tumor_OR1291
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 1044.77686 223.05094
AFFX-SNP_10009702 BB 342.80084 856.79058
AFFX-SNP_10015773 BB 1366.24639 2177.35697
AFFX-SNP_10021569 AA 754.40585 418.35054
AFFX-SNP_10026879 BB 593.38410 1723.00935
AFFX-SNP_10029725 AB 649.76480 554.51565
AFFX-SNP_10034687 BB 356.43159 1138.45875
AFFX-SNP_10036267 BB 320.02281 771.97593
AFFX-SNP_10037362 BB 908.44841 3341.50199
AFFX-SNP_10037636 BB 223.84157 712.41899
AFFX-SNP_10039349 BB 251.95236 1171.35369
AFFX-SNP_10039442 AA 1266.69304 210.95963
AFFX-SNP_10039933 BB 694.20644 2031.17268
AFFX-SNP_10046830 AB 1001.45973 1315.26263
AFFX-SNP_10047363 BB 326.49286 807.16950
AFFX-SNP_10047841 AB 977.95860 975.86278
AFFX-SNP_10049334 AB 1645.69175 1170.45681
AFFX-SNP_10052664 BB 258.63222 1089.96185
AFFX-SNP_10057887 AA 873.00543 360.73344
AFFX-SNP_10064911 AB 816.28432 689.00602

Total number of rows: 909622

Table truncated, full table size 33735 Kbytes.

Supplementary file Size Download File type/resource
GSM617683_OR1291.CEL.gz 33.0 Mb (ftp)(http) CEL
GSM617683_OR1291.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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