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Sample GSM617708 Query DataSets for GSM617708
Status Public on Sep 01, 2011
Title OSCC tumor_OR2341
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 759.23031 1778.35874
AFFX-SNP_10009702 AB 826.00893 688.09380
AFFX-SNP_10015773 AB 1499.36364 1569.63186
AFFX-SNP_10021569 AA 696.31744 337.68969
AFFX-SNP_10026879 BB 602.80968 1751.51537
AFFX-SNP_10029725 BB 354.00029 599.16787
AFFX-SNP_10034687 AA 808.89917 404.79594
AFFX-SNP_10036267 BB 355.47639 828.32479
AFFX-SNP_10037362 BB 931.97717 3459.66790
AFFX-SNP_10037636 BB 260.88078 769.94473
AFFX-SNP_10039349 BB 310.80788 1069.59607
AFFX-SNP_10039442 AA 1582.27040 234.60437
AFFX-SNP_10039933 BB 715.25427 1766.70984
AFFX-SNP_10046830 BB 229.67144 2120.98421
AFFX-SNP_10047363 BB 302.04386 895.24623
AFFX-SNP_10047841 AB 781.42764 764.98968
AFFX-SNP_10049334 BB 475.15024 1972.56253
AFFX-SNP_10052664 BB 234.85951 911.06789
AFFX-SNP_10057887 AB 535.09870 633.06263
AFFX-SNP_10064911 BB 400.31089 1256.42909

Total number of rows: 909622

Table truncated, full table size 33722 Kbytes.

Supplementary file Size Download File type/resource
GSM617708_OR2341.CEL.gz 33.1 Mb (ftp)(http) CEL
GSM617708_OR2341.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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