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Sample GSM617667 Query DataSets for GSM617667
Status Public on Sep 01, 2011
Title OSCC tumor_OR0948
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 AB 673.92837 1703.81162
AFFX-SNP_10009702 AB 783.04072 501.23323
AFFX-SNP_10015773 AB 1688.75505 1467.72237
AFFX-SNP_10021569 AB 531.44082 623.31631
AFFX-SNP_10026879 BB 633.33825 1945.88168
AFFX-SNP_10029725 AB 497.66211 479.79942
AFFX-SNP_10034687 AA 1103.06466 453.54697
AFFX-SNP_10036267 BB 356.40754 861.72116
AFFX-SNP_10037362 BB 986.08649 3518.78193
AFFX-SNP_10037636 BB 222.96798 916.01634
AFFX-SNP_10039349 BB 329.87733 1185.69400
AFFX-SNP_10039442 AA 1462.82145 224.04926
AFFX-SNP_10039933 BB 626.86136 1829.09362
AFFX-SNP_10046830 BB 291.14510 1812.13852
AFFX-SNP_10047363 AB 485.60868 471.82768
AFFX-SNP_10047841 AA 1252.42039 420.03655
AFFX-SNP_10049334 BB 404.23131 1991.75300
AFFX-SNP_10052664 BB 274.68677 984.08840
AFFX-SNP_10057887 AB 507.76128 591.43606
AFFX-SNP_10064911 AB 808.90928 712.83326

Total number of rows: 909622

Table truncated, full table size 33721 Kbytes.

Supplementary file Size Download File type/resource
GSM617667_OR0948.CEL.gz 33.0 Mb (ftp)(http) CEL
GSM617667_OR0948.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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