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Sample GSM617777 Query DataSets for GSM617777
Status Public on Sep 01, 2011
Title Normal oral tissue_ON78
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 989.80222 214.16460
AFFX-SNP_10009702 AB 818.11063 507.50085
AFFX-SNP_10015773 AB 1597.98312 1512.25265
AFFX-SNP_10021569 AA 727.48087 433.93258
AFFX-SNP_10026879 BB 604.36553 1563.92869
AFFX-SNP_10029725 AA 630.29144 295.91450
AFFX-SNP_10034687 AB 418.08143 814.78490
AFFX-SNP_10036267 AB 393.93622 502.80717
AFFX-SNP_10037362 BB 1109.15643 4014.99429
AFFX-SNP_10037636 BB 185.27423 749.39580
AFFX-SNP_10039349 AB 725.45370 648.56596
AFFX-SNP_10039442 AA 1493.23334 211.13277
AFFX-SNP_10039933 BB 745.54293 1839.02870
AFFX-SNP_10046830 BB 261.24026 1819.43856
AFFX-SNP_10047363 AB 572.79716 512.99157
AFFX-SNP_10047841 AB 866.36235 794.32479
AFFX-SNP_10049334 AB 1677.37047 1219.51120
AFFX-SNP_10052664 BB 265.28248 930.06064
AFFX-SNP_10057887 BB 259.46988 762.32914
AFFX-SNP_10064911 AB 709.76118 561.30680

Total number of rows: 909622

Table truncated, full table size 33730 Kbytes.

Supplementary file Size Download File type/resource
GSM617777_ON78.CEL.gz 34.5 Mb (ftp)(http) CEL
GSM617777_ON78.birdseed.chp.gz 13.2 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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