GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM617764 Query DataSets for GSM617764
Status Public on Sep 01, 2011
Title OSCC tumor_OR4119
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 1129.84971 190.90123
AFFX-SNP_10009702 BB 403.97540 943.11972
AFFX-SNP_10015773 NoCall 1345.09649 1647.52659
AFFX-SNP_10021569 AA 707.07002 446.48077
AFFX-SNP_10026879 AB 1572.42593 1366.97320
AFFX-SNP_10029725 BB 367.07901 649.62980
AFFX-SNP_10034687 AB 543.71765 791.39629
AFFX-SNP_10036267 BB 322.26096 889.78367
AFFX-SNP_10037362 BB 1014.15011 4051.71341
AFFX-SNP_10037636 AB 578.16752 521.57345
AFFX-SNP_10039349 BB 258.32574 1174.44741
AFFX-SNP_10039442 AA 1580.99516 187.05870
AFFX-SNP_10039933 BB 765.93346 2028.11383
AFFX-SNP_10046830 AA 1499.75565 308.24971
AFFX-SNP_10047363 BB 311.43423 562.63599
AFFX-SNP_10047841 AB 869.92531 807.94168
AFFX-SNP_10049334 AB 1642.81744 1260.80240
AFFX-SNP_10052664 AB 503.81825 646.98441
AFFX-SNP_10057887 BB 268.28247 761.58338
AFFX-SNP_10064911 AB 684.48031 695.78886

Total number of rows: 909622

Table truncated, full table size 33754 Kbytes.

Supplementary file Size Download File type/resource
GSM617764_OR4119.CEL.gz 32.6 Mb (ftp)(http) CEL
GSM617764_OR4119.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