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Sample GSM617670 Query DataSets for GSM617670
Status Public on Sep 01, 2011
Title OSCC tumor_OR0997
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 238.34443 1927.46032
AFFX-SNP_10009702 AA 1155.51601 275.80476
AFFX-SNP_10015773 AA 1976.77634 1232.49221
AFFX-SNP_10021569 AA 602.77448 427.03053
AFFX-SNP_10026879 BB 563.02248 2017.35160
AFFX-SNP_10029725 AA 732.82075 361.27225
AFFX-SNP_10034687 NoCall 787.22140 561.59515
AFFX-SNP_10036267 BB 336.41862 784.09667
AFFX-SNP_10037362 BB 937.12354 3385.70431
AFFX-SNP_10037636 BB 220.59018 678.86955
AFFX-SNP_10039349 AB 697.05599 718.67286
AFFX-SNP_10039442 AA 1296.92889 247.13915
AFFX-SNP_10039933 BB 736.98936 1869.89784
AFFX-SNP_10046830 AB 966.16621 1209.53786
AFFX-SNP_10047363 AB 510.70935 476.49116
AFFX-SNP_10047841 AB 739.75915 923.55388
AFFX-SNP_10049334 AA 2834.06103 641.47924
AFFX-SNP_10052664 AB 585.92660 624.91268
AFFX-SNP_10057887 AB 585.86109 639.79811
AFFX-SNP_10064911 AB 712.58096 1021.72252

Total number of rows: 909622

Table truncated, full table size 33751 Kbytes.

Supplementary file Size Download File type/resource
GSM617670_OR0997.CEL.gz 31.3 Mb (ftp)(http) CEL
GSM617670_OR0997.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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