GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM617769 Query DataSets for GSM617769
Status Public on Sep 01, 2011
Title OSCC tumor_OR4181
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 735.02157 1460.38400
AFFX-SNP_10009702 AB 839.02211 638.14232
AFFX-SNP_10015773 AB 1457.44915 1365.65211
AFFX-SNP_10021569 AA 737.74814 389.75937
AFFX-SNP_10026879 BB 636.01818 1915.86257
AFFX-SNP_10029725 BB 303.99549 529.30048
AFFX-SNP_10034687 AB 519.14918 845.08003
AFFX-SNP_10036267 BB 324.17297 757.40038
AFFX-SNP_10037362 BB 920.50217 3929.68990
AFFX-SNP_10037636 BB 229.29871 1083.67556
AFFX-SNP_10039349 BB 262.70320 1135.78639
AFFX-SNP_10039442 AA 1337.86013 219.02536
AFFX-SNP_10039933 BB 625.51685 2059.75510
AFFX-SNP_10046830 BB 267.70454 1639.52754
AFFX-SNP_10047363 AB 515.90473 426.72958
AFFX-SNP_10047841 AB 777.41413 852.57459
AFFX-SNP_10049334 AB 1686.59579 1195.57966
AFFX-SNP_10052664 BB 298.77165 907.06523
AFFX-SNP_10057887 AA 774.36929 378.74775
AFFX-SNP_10064911 AB 577.21119 586.64434

Total number of rows: 909622

Table truncated, full table size 33723 Kbytes.

Supplementary file Size Download File type/resource
GSM617769_OR4181.CEL.gz 33.9 Mb (ftp)(http) CEL
GSM617769_OR4181.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