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Sample GSM617773 Query DataSets for GSM617773
Status Public on Sep 01, 2011
Title Normal oral tissue_ON57
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 AB 669.66863 1262.07500
AFFX-SNP_10009702 AA 1163.84733 301.86268
AFFX-SNP_10015773 AB 1438.20066 1481.31504
AFFX-SNP_10021569 AA 851.83790 471.97236
AFFX-SNP_10026879 AA 1916.22632 614.23755
AFFX-SNP_10029725 AB 496.57215 443.57399
AFFX-SNP_10034687 AA 960.77338 380.47886
AFFX-SNP_10036267 AA 574.13260 265.28720
AFFX-SNP_10037362 BB 853.99553 3645.60245
AFFX-SNP_10037636 BB 169.71920 1073.95693
AFFX-SNP_10039349 BB 267.42112 1086.07820
AFFX-SNP_10039442 AA 1406.41362 199.48119
AFFX-SNP_10039933 BB 578.49085 1840.79935
AFFX-SNP_10046830 BB 259.85562 1817.41432
AFFX-SNP_10047363 BB 404.29225 819.03173
AFFX-SNP_10047841 AA 1052.37676 329.59298
AFFX-SNP_10049334 AB 1618.87431 1223.33441
AFFX-SNP_10052664 BB 300.01103 1200.25405
AFFX-SNP_10057887 AB 591.91802 596.27593
AFFX-SNP_10064911 AB 598.45814 684.97566

Total number of rows: 909622

Table truncated, full table size 33723 Kbytes.

Supplementary file Size Download File type/resource
GSM617773_ON57.CEL.gz 33.3 Mb (ftp)(http) CEL
GSM617773_ON57.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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