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Sample GSM617711 Query DataSets for GSM617711
Status Public on Sep 01, 2011
Title OSCC tumor_OR2360
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 BB 301.59531 2103.11440
AFFX-SNP_10009702 AA 1088.47739 265.46084
AFFX-SNP_10015773 AA 1915.84097 869.37946
AFFX-SNP_10021569 AA 722.73263 370.20668
AFFX-SNP_10026879 AA 2050.40008 632.91369
AFFX-SNP_10029725 AB 492.30122 456.88055
AFFX-SNP_10034687 AA 554.86924 357.02746
AFFX-SNP_10036267 BB 343.25690 853.97259
AFFX-SNP_10037362 BB 1041.17957 4149.24672
AFFX-SNP_10037636 BB 213.93570 800.53680
AFFX-SNP_10039349 BB 285.37063 1097.90551
AFFX-SNP_10039442 AA 1373.63133 191.27064
AFFX-SNP_10039933 BB 737.16974 2125.69430
AFFX-SNP_10046830 AA 1455.50363 294.99308
AFFX-SNP_10047363 AA 773.57653 170.51592
AFFX-SNP_10047841 AA 1241.18504 416.16298
AFFX-SNP_10049334 AB 2065.00004 1582.38101
AFFX-SNP_10052664 BB 286.75190 967.93900
AFFX-SNP_10057887 AB 596.94441 735.45670
AFFX-SNP_10064911 AB 602.75950 731.78433

Total number of rows: 909622

Table truncated, full table size 33766 Kbytes.

Supplementary file Size Download File type/resource
GSM617711_OR2360.CEL.gz 33.3 Mb (ftp)(http) CEL
GSM617711_OR2360.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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