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Sample GSM617712 Query DataSets for GSM617712
Status Public on Sep 01, 2011
Title OSCC tumor_OR2378
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 1220.39765 287.21419
AFFX-SNP_10009702 AA 1415.21037 283.32265
AFFX-SNP_10015773 NoCall 1796.97138 1322.86357
AFFX-SNP_10021569 NoCall 672.11271 518.32409
AFFX-SNP_10026879 AB 1548.94844 1254.30480
AFFX-SNP_10029725 AB 526.52381 463.94996
AFFX-SNP_10034687 AA 1097.56791 540.58504
AFFX-SNP_10036267 AB 420.96283 632.91153
AFFX-SNP_10037362 BB 990.98688 3566.99980
AFFX-SNP_10037636 BB 204.27563 784.27484
AFFX-SNP_10039349 AB 737.46973 688.46460
AFFX-SNP_10039442 AA 1328.86782 196.61658
AFFX-SNP_10039933 BB 737.26777 1863.56635
AFFX-SNP_10046830 BB 282.42669 2095.88835
AFFX-SNP_10047363 BB 335.05273 779.72138
AFFX-SNP_10047841 BB 655.60059 1264.64954
AFFX-SNP_10049334 AA 2672.97031 560.88973
AFFX-SNP_10052664 BB 323.51280 941.74617
AFFX-SNP_10057887 AB 456.13263 604.06689
AFFX-SNP_10064911 AB 850.83770 632.51913

Total number of rows: 909622

Table truncated, full table size 33771 Kbytes.

Supplementary file Size Download File type/resource
GSM617712_OR2378.CEL.gz 32.6 Mb (ftp)(http) CEL
GSM617712_OR2378.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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