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Sample GSM617662 Query DataSets for GSM617662
Status Public on Sep 01, 2011
Title OSCC tumor_OR0811
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 764.43061 1702.72232
AFFX-SNP_10009702 AA 1226.45835 273.74310
AFFX-SNP_10015773 BB 1265.08556 2212.61313
AFFX-SNP_10021569 AA 861.32104 462.13422
AFFX-SNP_10026879 AB 1620.11136 1290.86805
AFFX-SNP_10029725 BB 363.11958 652.85943
AFFX-SNP_10034687 AB 547.24638 827.02537
AFFX-SNP_10036267 BB 368.92401 881.06985
AFFX-SNP_10037362 BB 1013.11850 3678.46218
AFFX-SNP_10037636 BB 265.88186 883.36796
AFFX-SNP_10039349 BB 291.51310 1147.21618
AFFX-SNP_10039442 AA 1566.41191 233.81650
AFFX-SNP_10039933 BB 757.42188 1789.71493
AFFX-SNP_10046830 BB 284.77300 1960.48492
AFFX-SNP_10047363 AB 572.96864 490.84845
AFFX-SNP_10047841 AB 823.83928 909.52658
AFFX-SNP_10049334 AA 2736.11576 595.91629
AFFX-SNP_10052664 BB 344.76385 1044.83942
AFFX-SNP_10057887 BB 273.61159 930.94115
AFFX-SNP_10064911 AA 964.28322 266.60715

Total number of rows: 909622

Table truncated, full table size 33720 Kbytes.

Supplementary file Size Download File type/resource
GSM617662_OR0811.CEL.gz 32.3 Mb (ftp)(http) CEL
GSM617662_OR0811.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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