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Sample GSM617778 Query DataSets for GSM617778
Status Public on Sep 01, 2011
Title Normal oral tissue_ON79
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 1063.06562 233.70861
AFFX-SNP_10009702 AA 1168.23329 282.86624
AFFX-SNP_10015773 AA 1811.97502 849.09289
AFFX-SNP_10021569 AA 623.78624 373.88917
AFFX-SNP_10026879 BB 615.63837 1617.08362
AFFX-SNP_10029725 AB 504.87180 442.97228
AFFX-SNP_10034687 AB 730.30869 840.05908
AFFX-SNP_10036267 AB 481.65416 510.96706
AFFX-SNP_10037362 BB 998.40606 3628.92774
AFFX-SNP_10037636 BB 218.29050 819.14618
AFFX-SNP_10039349 BB 291.32587 1059.96290
AFFX-SNP_10039442 AA 1431.11793 226.94024
AFFX-SNP_10039933 BB 783.26545 1886.23063
AFFX-SNP_10046830 AB 927.45312 1151.61404
AFFX-SNP_10047363 AB 523.19360 531.05065
AFFX-SNP_10047841 AB 842.52811 835.51165
AFFX-SNP_10049334 AB 1894.71974 1309.99078
AFFX-SNP_10052664 BB 293.62706 1011.87664
AFFX-SNP_10057887 BB 322.47511 783.13803
AFFX-SNP_10064911 BB 379.63726 888.83538

Total number of rows: 909622

Table truncated, full table size 33722 Kbytes.

Supplementary file Size Download File type/resource
GSM617778_ON79.CEL.gz 33.5 Mb (ftp)(http) CEL
GSM617778_ON79.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

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