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Sample GSM617688 Query DataSets for GSM617688
Status Public on Sep 01, 2011
Title OSCC tumor_OR1349
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 764.71467 1521.60761
AFFX-SNP_10009702 AB 796.33731 487.45702
AFFX-SNP_10015773 AA 2062.74393 1156.26566
AFFX-SNP_10021569 AA 652.50515 433.58120
AFFX-SNP_10026879 BB 775.69192 1967.93985
AFFX-SNP_10029725 AB 783.32434 552.48238
AFFX-SNP_10034687 AA 1160.64474 469.70467
AFFX-SNP_10036267 BB 412.98200 898.12425
AFFX-SNP_10037362 BB 998.20970 3602.18083
AFFX-SNP_10037636 BB 202.62465 811.04768
AFFX-SNP_10039349 AA 1142.05370 270.61337
AFFX-SNP_10039442 AA 1629.93847 188.42574
AFFX-SNP_10039933 BB 816.64771 1974.54884
AFFX-SNP_10046830 BB 306.30296 2156.68524
AFFX-SNP_10047363 AB 597.44492 494.85771
AFFX-SNP_10047841 AA 1232.98473 432.37305
AFFX-SNP_10049334 BB 600.54529 2026.02195
AFFX-SNP_10052664 BB 371.43990 1115.78642
AFFX-SNP_10057887 AB 590.34169 658.23482
AFFX-SNP_10064911 AB 786.17207 724.35848

Total number of rows: 909622

Table truncated, full table size 33755 Kbytes.

Supplementary file Size Download File type/resource
GSM617688_OR1349.CEL.gz 31.6 Mb (ftp)(http) CEL
GSM617688_OR1349.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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