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Sample GSM617718 Query DataSets for GSM617718
Status Public on Sep 01, 2011
Title OSCC tumor_OR2461
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 1148.38322 262.93516
AFFX-SNP_10009702 AB 730.60304 493.15186
AFFX-SNP_10015773 AB 1638.31769 1693.52604
AFFX-SNP_10021569 AA 683.77192 370.98696
AFFX-SNP_10026879 AA 1835.99267 761.69864
AFFX-SNP_10029725 BB 386.08899 541.06350
AFFX-SNP_10034687 AB 868.88581 876.33435
AFFX-SNP_10036267 BB 287.41736 846.90692
AFFX-SNP_10037362 BB 1027.50082 3587.33659
AFFX-SNP_10037636 BB 194.20676 820.98098
AFFX-SNP_10039349 BB 317.95778 1046.05469
AFFX-SNP_10039442 AA 1398.53658 166.14994
AFFX-SNP_10039933 AB 1241.58924 1263.73862
AFFX-SNP_10046830 AB 912.31347 1418.87668
AFFX-SNP_10047363 BB 300.22171 586.62337
AFFX-SNP_10047841 AB 1030.41948 847.98425
AFFX-SNP_10049334 AB 1611.98005 1407.89245
AFFX-SNP_10052664 BB 266.44341 1063.18091
AFFX-SNP_10057887 BB 329.22933 770.82834
AFFX-SNP_10064911 AA 855.63604 270.83328

Total number of rows: 909622

Table truncated, full table size 33735 Kbytes.

Supplementary file Size Download File type/resource
GSM617718_OR2461.CEL.gz 33.0 Mb (ftp)(http) CEL
GSM617718_OR2461.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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