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Sample GSM617770 Query DataSets for GSM617770
Status Public on Sep 01, 2011
Title OSCC tumor_OR4199
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 780.84336 1471.35161
AFFX-SNP_10009702 AA 1528.86003 284.51917
AFFX-SNP_10015773 AA 1647.65728 926.91334
AFFX-SNP_10021569 AA 709.29387 335.74220
AFFX-SNP_10026879 BB 614.12105 1669.03917
AFFX-SNP_10029725 AB 596.38735 441.83890
AFFX-SNP_10034687 AA 1097.87915 346.38933
AFFX-SNP_10036267 AB 431.62496 539.64755
AFFX-SNP_10037362 BB 951.14800 3502.17733
AFFX-SNP_10037636 BB 222.95440 953.29576
AFFX-SNP_10039349 AB 890.27392 804.92523
AFFX-SNP_10039442 AA 1289.06427 208.91558
AFFX-SNP_10039933 BB 615.57909 1858.93665
AFFX-SNP_10046830 AB 824.01273 1179.86058
AFFX-SNP_10047363 BB 298.85576 737.50527
AFFX-SNP_10047841 AA 1141.71710 338.08078
AFFX-SNP_10049334 AB 1623.02683 1186.55060
AFFX-SNP_10052664 BB 255.70748 872.80570
AFFX-SNP_10057887 AB 557.24052 603.72914
AFFX-SNP_10064911 AB 696.23986 600.32704

Total number of rows: 909622

Table truncated, full table size 33737 Kbytes.

Supplementary file Size Download File type/resource
GSM617770_OR4199.CEL.gz 33.5 Mb (ftp)(http) CEL
GSM617770_OR4199.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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