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Sample GSM617664 Query DataSets for GSM617664
Status Public on Sep 01, 2011
Title OSCC tumor_OR0918
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 AA 1254.20787 208.64886
AFFX-SNP_10009702 AB 744.02933 571.12482
AFFX-SNP_10015773 AB 1728.99667 1617.09543
AFFX-SNP_10021569 AA 917.43222 386.71219
AFFX-SNP_10026879 AB 1419.68404 1398.30502
AFFX-SNP_10029725 AB 507.19961 446.68668
AFFX-SNP_10034687 AA 643.56461 383.09979
AFFX-SNP_10036267 AB 427.08220 564.51078
AFFX-SNP_10037362 BB 1065.26481 3711.41725
AFFX-SNP_10037636 AB 541.77473 384.57418
AFFX-SNP_10039349 BB 300.18581 914.72665
AFFX-SNP_10039442 AA 1319.82143 215.30333
AFFX-SNP_10039933 BB 719.57642 2195.40784
AFFX-SNP_10046830 BB 235.79796 2103.79849
AFFX-SNP_10047363 AB 540.24292 583.69538
AFFX-SNP_10047841 AA 1086.54260 343.71965
AFFX-SNP_10049334 BB 356.15093 1638.36752
AFFX-SNP_10052664 BB 294.08729 795.71878
AFFX-SNP_10057887 BB 277.20787 873.78784
AFFX-SNP_10064911 AB 802.53047 640.01242

Total number of rows: 909622

Table truncated, full table size 33752 Kbytes.

Supplementary file Size Download File type/resource
GSM617664_OR0918.CEL.gz 33.0 Mb (ftp)(http) CEL
GSM617664_OR0918.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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