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Sample GSM617707 Query DataSets for GSM617707
Status Public on Sep 01, 2011
Title OSCC tumor_OR2332
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 AA 1132.75837 212.96564
AFFX-SNP_10009702 AA 1353.14009 259.80291
AFFX-SNP_10015773 AA 1892.67892 1114.02300
AFFX-SNP_10021569 AA 818.62955 411.85509
AFFX-SNP_10026879 AB 1337.02760 1477.76122
AFFX-SNP_10029725 BB 401.31125 604.94276
AFFX-SNP_10034687 AA 1359.76704 440.19840
AFFX-SNP_10036267 AB 487.76738 581.75146
AFFX-SNP_10037362 BB 1038.04324 3489.24240
AFFX-SNP_10037636 BB 193.01310 942.01549
AFFX-SNP_10039349 AB 719.16906 666.84957
AFFX-SNP_10039442 AA 1389.49103 193.51144
AFFX-SNP_10039933 BB 725.64350 1905.40920
AFFX-SNP_10046830 AB 734.55977 1049.17494
AFFX-SNP_10047363 BB 298.44776 533.26676
AFFX-SNP_10047841 AB 1081.39162 890.45928
AFFX-SNP_10049334 BB 444.37876 1490.78668
AFFX-SNP_10052664 BB 371.46360 1232.09391
AFFX-SNP_10057887 AB 554.39176 646.52821
AFFX-SNP_10064911 AB 674.11493 580.16657

Total number of rows: 909622

Table truncated, full table size 33757 Kbytes.

Supplementary file Size Download File type/resource
GSM617707_OR2332.CEL.gz 31.4 Mb (ftp)(http) CEL
GSM617707_OR2332.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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