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Sample GSM617772 Query DataSets for GSM617772
Status Public on Sep 01, 2011
Title Normal oral tissue_ON51
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 689.09920 1565.69226
AFFX-SNP_10009702 AA 1036.49776 295.56654
AFFX-SNP_10015773 AB 1427.93462 1448.69239
AFFX-SNP_10021569 AA 751.28558 348.88049
AFFX-SNP_10026879 BB 678.33733 1827.12086
AFFX-SNP_10029725 BB 353.11693 543.20016
AFFX-SNP_10034687 AA 1060.60700 474.92100
AFFX-SNP_10036267 BB 314.37537 741.55884
AFFX-SNP_10037362 BB 966.51112 3747.30354
AFFX-SNP_10037636 BB 209.41834 949.02298
AFFX-SNP_10039349 AB 799.62639 683.60671
AFFX-SNP_10039442 AA 1516.77605 231.56536
AFFX-SNP_10039933 BB 671.20115 1960.02733
AFFX-SNP_10046830 AB 882.11430 1045.26190
AFFX-SNP_10047363 AB 484.30115 431.80801
AFFX-SNP_10047841 AB 915.37673 949.03768
AFFX-SNP_10049334 AB 1840.33215 1346.31092
AFFX-SNP_10052664 BB 246.85287 986.78034
AFFX-SNP_10057887 AB 643.92120 668.13155
AFFX-SNP_10064911 AA 838.06162 280.81463

Total number of rows: 909622

Table truncated, full table size 33721 Kbytes.

Supplementary file Size Download File type/resource
GSM617772_ON51.CEL.gz 33.2 Mb (ftp)(http) CEL
GSM617772_ON51.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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