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Sample GSM617716 Query DataSets for GSM617716
Status Public on Sep 01, 2011
Title OSCC tumor_OR2449
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 954.05535 1643.17045
AFFX-SNP_10009702 AB 1067.64435 623.32928
AFFX-SNP_10015773 AA 1765.39132 934.58549
AFFX-SNP_10021569 AA 800.21602 369.74024
AFFX-SNP_10026879 AB 1429.06617 1538.47362
AFFX-SNP_10029725 AB 551.51307 520.97849
AFFX-SNP_10034687 AB 884.02998 912.29049
AFFX-SNP_10036267 BB 370.16462 859.87382
AFFX-SNP_10037362 BB 1005.30480 4090.22280
AFFX-SNP_10037636 BB 198.73031 773.51979
AFFX-SNP_10039349 BB 381.67745 1145.72756
AFFX-SNP_10039442 AA 1653.57179 215.14433
AFFX-SNP_10039933 BB 789.95700 2166.11511
AFFX-SNP_10046830 AB 914.14840 965.47953
AFFX-SNP_10047363 BB 331.13412 782.78497
AFFX-SNP_10047841 AB 1007.42358 1090.98011
AFFX-SNP_10049334 BB 871.11812 2027.45899
AFFX-SNP_10052664 BB 352.09666 1103.45250
AFFX-SNP_10057887 AB 526.17892 700.82195
AFFX-SNP_10064911 AB 747.46106 880.92792

Total number of rows: 909622

Table truncated, full table size 33795 Kbytes.

Supplementary file Size Download File type/resource
GSM617716_OR2449.CEL.gz 33.1 Mb (ftp)(http) CEL
GSM617716_OR2449.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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