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Sample GSM617706 Query DataSets for GSM617706
Status Public on Sep 01, 2011
Title OSCC tumor_OR2328
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 333.19210 2661.40878
AFFX-SNP_10009702 AB 837.53695 539.57625
AFFX-SNP_10015773 AB 1581.88169 1606.25680
AFFX-SNP_10021569 AA 779.26370 453.60330
AFFX-SNP_10026879 BB 588.45853 1652.12270
AFFX-SNP_10029725 AB 542.53620 518.43061
AFFX-SNP_10034687 AA 1387.89481 441.18675
AFFX-SNP_10036267 AB 447.95817 588.17299
AFFX-SNP_10037362 BB 849.47400 3491.14783
AFFX-SNP_10037636 BB 204.14531 834.32195
AFFX-SNP_10039349 AB 971.81207 761.47128
AFFX-SNP_10039442 AA 1348.24338 221.10500
AFFX-SNP_10039933 BB 633.27896 1906.55248
AFFX-SNP_10046830 AB 883.52143 1152.44824
AFFX-SNP_10047363 AB 494.41033 548.73147
AFFX-SNP_10047841 BB 524.45216 1513.58411
AFFX-SNP_10049334 AB 2058.91864 1153.21958
AFFX-SNP_10052664 BB 254.67722 1114.52135
AFFX-SNP_10057887 BB 283.37677 855.27608
AFFX-SNP_10064911 BB 405.41384 1087.53348

Total number of rows: 909622

Table truncated, full table size 33725 Kbytes.

Supplementary file Size Download File type/resource
GSM617706_OR2328.CEL.gz 32.5 Mb (ftp)(http) CEL
GSM617706_OR2328.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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