GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM617779 Query DataSets for GSM617779
Status Public on Sep 01, 2011
Title Normal oral tissue_ON80
Sample type genomic
Source name Normal oral tissue
Organism Homo sapiens
Characteristics disease state: norml
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 1110.19831 213.48918
AFFX-SNP_10009702 AA 1290.80802 244.76058
AFFX-SNP_10015773 AB 1478.20879 1325.28372
AFFX-SNP_10021569 AA 847.29967 398.99881
AFFX-SNP_10026879 BB 595.16529 1683.39474
AFFX-SNP_10029725 AB 501.57995 369.89530
AFFX-SNP_10034687 AB 869.04562 778.27718
AFFX-SNP_10036267 BB 329.22832 812.59392
AFFX-SNP_10037362 BB 925.78857 3881.52375
AFFX-SNP_10037636 BB 217.41609 938.48894
AFFX-SNP_10039349 AB 805.61090 683.07099
AFFX-SNP_10039442 AA 1411.18358 207.03679
AFFX-SNP_10039933 BB 654.46671 1819.64628
AFFX-SNP_10046830 AB 948.88586 1048.38008
AFFX-SNP_10047363 BB 252.28523 746.47013
AFFX-SNP_10047841 AB 839.13248 818.18404
AFFX-SNP_10049334 AA 2960.02439 436.44243
AFFX-SNP_10052664 BB 278.05882 977.44339
AFFX-SNP_10057887 AA 925.00375 351.28763
AFFX-SNP_10064911 AB 610.69382 552.68694

Total number of rows: 909622

Table truncated, full table size 33722 Kbytes.

Supplementary file Size Download File type/resource
GSM617779_ON80.CEL.gz 34.0 Mb (ftp)(http) CEL
GSM617779_ON80.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