GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM617760 Query DataSets for GSM617760
Status Public on Sep 01, 2011
Title OSCC tumor_OR4060
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 887.49928 200.22223
AFFX-SNP_10009702 BB 266.53119 977.78460
AFFX-SNP_10015773 AA 1855.79851 1200.23195
AFFX-SNP_10021569 AA 764.88088 489.09954
AFFX-SNP_10026879 BB 575.60732 2021.26040
AFFX-SNP_10029725 BB 374.10337 527.91423
AFFX-SNP_10034687 AA 1225.18746 431.03409
AFFX-SNP_10036267 BB 284.17322 782.43576
AFFX-SNP_10037362 BB 1070.89648 3637.63141
AFFX-SNP_10037636 BB 186.09350 702.63187
AFFX-SNP_10039349 AB 796.09855 584.92793
AFFX-SNP_10039442 AA 1315.37285 148.21226
AFFX-SNP_10039933 BB 938.29578 1898.59786
AFFX-SNP_10046830 BB 289.70774 1612.69114
AFFX-SNP_10047363 BB 378.82397 612.03353
AFFX-SNP_10047841 AB 842.51752 751.73732
AFFX-SNP_10049334 BB 472.27305 1942.04772
AFFX-SNP_10052664 BB 287.37223 884.42483
AFFX-SNP_10057887 BB 221.59531 661.40302
AFFX-SNP_10064911 NoCall 528.72405 911.65054

Total number of rows: 909622

Table truncated, full table size 33770 Kbytes.

Supplementary file Size Download File type/resource
GSM617760_OR4060.CEL.gz 32.6 Mb (ftp)(http) CEL
GSM617760_OR4060.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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap