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Sample GSM617771 Query DataSets for GSM617771
Status Public on Sep 01, 2011
Title OSCC tumor_OR4207
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 1137.03696 222.35261
AFFX-SNP_10009702 AA 1507.70691 251.31537
AFFX-SNP_10015773 AB 1471.20071 1478.44118
AFFX-SNP_10021569 AA 601.10563 360.18707
AFFX-SNP_10026879 BB 607.45387 1706.95999
AFFX-SNP_10029725 BB 376.91091 534.12453
AFFX-SNP_10034687 AA 1179.25883 388.97119
AFFX-SNP_10036267 AB 512.49702 529.98049
AFFX-SNP_10037362 BB 900.52597 3540.43737
AFFX-SNP_10037636 AB 638.83282 622.60063
AFFX-SNP_10039349 AB 788.25884 766.61786
AFFX-SNP_10039442 AA 1616.34573 194.39986
AFFX-SNP_10039933 AB 1252.44750 1223.25433
AFFX-SNP_10046830 AB 857.45253 1096.18933
AFFX-SNP_10047363 BB 298.36446 779.44021
AFFX-SNP_10047841 AB 872.46387 774.12171
AFFX-SNP_10049334 AB 1657.79413 1108.57869
AFFX-SNP_10052664 BB 287.13195 999.07666
AFFX-SNP_10057887 BB 221.62243 715.60849
AFFX-SNP_10064911 AB 658.80747 569.09155

Total number of rows: 909622

Table truncated, full table size 33718 Kbytes.

Supplementary file Size Download File type/resource
GSM617771_OR4207.CEL.gz 33.8 Mb (ftp)(http) CEL
GSM617771_OR4207.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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