GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM617755 Query DataSets for GSM617755
Status Public on Sep 01, 2011
Title OSCC tumor_OR4032
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 1002.55876 235.66912
AFFX-SNP_10009702 AB 1238.94466 484.54944
AFFX-SNP_10015773 AA 1753.31700 946.08785
AFFX-SNP_10021569 AA 674.06138 386.26514
AFFX-SNP_10026879 BB 560.74438 1637.07932
AFFX-SNP_10029725 AA 641.54491 296.89183
AFFX-SNP_10034687 AB 663.14936 976.98603
AFFX-SNP_10036267 AA 531.26693 275.08797
AFFX-SNP_10037362 BB 906.81218 3634.36297
AFFX-SNP_10037636 AB 500.72949 440.06102
AFFX-SNP_10039349 BB 300.13453 1159.18698
AFFX-SNP_10039442 AA 1541.41651 184.12088
AFFX-SNP_10039933 BB 601.84020 1520.85577
AFFX-SNP_10046830 BB 271.47036 1746.71635
AFFX-SNP_10047363 BB 347.01327 787.73739
AFFX-SNP_10047841 AA 1110.49135 317.51167
AFFX-SNP_10049334 AB 2219.25203 1364.58219
AFFX-SNP_10052664 BB 288.06826 1167.73378
AFFX-SNP_10057887 BB 307.52870 790.34580
AFFX-SNP_10064911 AA 912.64492 255.41025

Total number of rows: 909622

Table truncated, full table size 33745 Kbytes.

Supplementary file Size Download File type/resource
GSM617755_OR4032.CEL.gz 32.9 Mb (ftp)(http) CEL
GSM617755_OR4032.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