GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM617671 Query DataSets for GSM617671
Status Public on Sep 01, 2011
Title OSCC tumor_OR1008
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 978.39406 243.19851
AFFX-SNP_10009702 AA 978.57853 268.92146
AFFX-SNP_10015773 AA 2151.90947 1098.64792
AFFX-SNP_10021569 AA 643.14979 375.65781
AFFX-SNP_10026879 BB 621.62729 1917.54508
AFFX-SNP_10029725 BB 398.07845 622.64391
AFFX-SNP_10034687 AA 1139.74407 450.72857
AFFX-SNP_10036267 AB 566.86847 568.84638
AFFX-SNP_10037362 BB 978.86574 3535.38379
AFFX-SNP_10037636 BB 238.37816 897.02981
AFFX-SNP_10039349 AB 702.25664 514.81262
AFFX-SNP_10039442 AA 1533.79313 209.98328
AFFX-SNP_10039933 BB 713.57035 1815.94253
AFFX-SNP_10046830 BB 260.39680 1779.74010
AFFX-SNP_10047363 AA 764.40228 198.15095
AFFX-SNP_10047841 BB 684.24824 1451.92669
AFFX-SNP_10049334 AA 2612.23399 511.52609
AFFX-SNP_10052664 BB 285.89548 945.84311
AFFX-SNP_10057887 AA 858.36839 501.48881
AFFX-SNP_10064911 BB 588.78280 1150.23177

Total number of rows: 909622

Table truncated, full table size 33732 Kbytes.

Supplementary file Size Download File type/resource
GSM617671_OR1008.CEL.gz 31.8 Mb (ftp)(http) CEL
GSM617671_OR1008.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

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