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Sample GSM617661 Query DataSets for GSM617661
Status Public on Sep 01, 2011
Title OSCC tumor_OR0752
Sample type genomic
Source name OSCC specimens
Organism Homo sapiens
Characteristics disease state: tumor
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 768.59302 1760.82861
AFFX-SNP_10009702 BB 493.33322 729.69717
AFFX-SNP_10015773 AB 1891.41302 1923.25257
AFFX-SNP_10021569 AA 742.01250 396.40761
AFFX-SNP_10026879 AB 1687.69717 1506.86143
AFFX-SNP_10029725 BB 405.07453 720.41506
AFFX-SNP_10034687 NoCall 906.97626 592.28797
AFFX-SNP_10036267 BB 359.78248 951.00577
AFFX-SNP_10037362 BB 1078.82453 3685.40277
AFFX-SNP_10037636 BB 183.64224 903.35696
AFFX-SNP_10039349 BB 302.55203 1162.32444
AFFX-SNP_10039442 AA 1437.89966 230.07386
AFFX-SNP_10039933 AB 1386.85190 1431.44031
AFFX-SNP_10046830 AB 837.30257 1137.66806
AFFX-SNP_10047363 AA 704.48848 279.70314
AFFX-SNP_10047841 BB 695.12404 1363.89271
AFFX-SNP_10049334 AB 1710.64139 1386.03025
AFFX-SNP_10052664 BB 378.20916 955.74149
AFFX-SNP_10057887 AB 560.46776 599.55089
AFFX-SNP_10064911 AA 1133.61276 329.43970

Total number of rows: 909622

Table truncated, full table size 33769 Kbytes.

Supplementary file Size Download File type/resource
GSM617661_OR0752.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM617661_OR0752.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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