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Sample GSM617761 Query DataSets for GSM617761
Status Public on Sep 01, 2011
Title OSCC tumor_OR4070
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 894.99567 295.23467
AFFX-SNP_10009702 BB 361.81295 1075.00798
AFFX-SNP_10015773 AA 1915.28202 1199.57193
AFFX-SNP_10021569 AB 639.56667 544.84426
AFFX-SNP_10026879 BB 598.85928 1992.19878
AFFX-SNP_10029725 BB 465.08671 656.44667
AFFX-SNP_10034687 AA 1020.10093 597.66910
AFFX-SNP_10036267 BB 430.49496 829.83811
AFFX-SNP_10037362 BB 916.83632 3725.22404
AFFX-SNP_10037636 BB 223.64905 994.64473
AFFX-SNP_10039349 AB 676.70513 647.16221
AFFX-SNP_10039442 AA 1432.23257 227.35367
AFFX-SNP_10039933 BB 801.02166 2063.88993
AFFX-SNP_10046830 BB 224.20843 1562.60135
AFFX-SNP_10047363 BB 301.37284 611.70634
AFFX-SNP_10047841 AB 979.85385 788.21147
AFFX-SNP_10049334 BB 530.51942 2047.51590
AFFX-SNP_10052664 BB 320.90868 1037.24670
AFFX-SNP_10057887 BB 286.20154 949.50285
AFFX-SNP_10064911 BB 465.14337 1170.47979

Total number of rows: 909622

Table truncated, full table size 33750 Kbytes.

Supplementary file Size Download File type/resource
GSM617761_OR4070.CEL.gz 30.8 Mb (ftp)(http) CEL
GSM617761_OR4070.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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