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Sample GSM617766 Query DataSets for GSM617766
Status Public on Sep 01, 2011
Title OSCC tumor_OR4145
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 576.26388 1958.51436
AFFX-SNP_10009702 AA 1427.60627 283.96303
AFFX-SNP_10015773 AA 1718.30053 980.70739
AFFX-SNP_10021569 AA 679.70555 363.77521
AFFX-SNP_10026879 AB 1325.76865 1212.31632
AFFX-SNP_10029725 BB 381.00395 548.86549
AFFX-SNP_10034687 AA 1267.12554 405.71484
AFFX-SNP_10036267 AB 429.51792 563.41990
AFFX-SNP_10037362 BB 992.50761 3196.10984
AFFX-SNP_10037636 BB 236.84948 887.84290
AFFX-SNP_10039349 BB 282.30800 1295.55896
AFFX-SNP_10039442 AA 1461.38234 156.70906
AFFX-SNP_10039933 BB 666.72964 2006.57032
AFFX-SNP_10046830 BB 243.31017 1653.99966
AFFX-SNP_10047363 AA 717.12223 237.08145
AFFX-SNP_10047841 BB 656.81197 1356.34141
AFFX-SNP_10049334 BB 369.80699 1865.52675
AFFX-SNP_10052664 BB 282.38077 1081.61234
AFFX-SNP_10057887 AB 443.92627 546.02601
AFFX-SNP_10064911 AB 687.04848 547.59702

Total number of rows: 909622

Table truncated, full table size 33743 Kbytes.

Supplementary file Size Download File type/resource
GSM617766_OR4145.CEL.gz 32.8 Mb (ftp)(http) CEL
GSM617766_OR4145.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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