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Sample GSM617660 Query DataSets for GSM617660
Status Public on Sep 01, 2011
Title OSCC tumor_OR0265
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 643.09658 1539.63826
AFFX-SNP_10009702 AB 875.63706 540.65403
AFFX-SNP_10015773 AA 1625.39826 1005.10445
AFFX-SNP_10021569 AA 830.23879 374.95382
AFFX-SNP_10026879 BB 574.39474 1765.62438
AFFX-SNP_10029725 AB 543.56253 468.07852
AFFX-SNP_10034687 AA 914.63543 423.08634
AFFX-SNP_10036267 BB 297.72064 754.03027
AFFX-SNP_10037362 BB 1043.96084 4442.05195
AFFX-SNP_10037636 AB 546.05404 605.56789
AFFX-SNP_10039349 BB 278.46734 1154.11712
AFFX-SNP_10039442 AA 1532.16395 255.66875
AFFX-SNP_10039933 AB 1273.45228 1295.95541
AFFX-SNP_10046830 AA 1729.17507 283.52046
AFFX-SNP_10047363 AB 722.80814 483.23085
AFFX-SNP_10047841 AB 791.34302 660.24053
AFFX-SNP_10049334 BB 424.68453 2049.26272
AFFX-SNP_10052664 BB 291.50454 890.12292
AFFX-SNP_10057887 AB 674.50610 560.27396
AFFX-SNP_10064911 BB 427.06888 1192.64973

Total number of rows: 909622

Table truncated, full table size 33741 Kbytes.

Supplementary file Size Download File type/resource
GSM617660_OR0265.CEL.gz 32.8 Mb (ftp)(http) CEL
GSM617660_OR0265.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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