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Sample GSM617689 Query DataSets for GSM617689
Status Public on Sep 01, 2011
Title OSCC tumor_OR1376
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 1041.30825 206.05998
AFFX-SNP_10009702 AA 1156.33473 284.63769
AFFX-SNP_10015773 AA 1896.97963 1156.25559
AFFX-SNP_10021569 AA 698.30868 431.15335
AFFX-SNP_10026879 AB 1400.06880 1408.24906
AFFX-SNP_10029725 AB 619.80271 467.32963
AFFX-SNP_10034687 AB 985.40131 997.56990
AFFX-SNP_10036267 BB 372.57295 816.73139
AFFX-SNP_10037362 BB 1087.75339 4025.28893
AFFX-SNP_10037636 AB 546.31476 666.24586
AFFX-SNP_10039349 BB 290.90496 982.89491
AFFX-SNP_10039442 AA 1520.56274 192.98487
AFFX-SNP_10039933 BB 719.80077 2047.13750
AFFX-SNP_10046830 BB 277.37050 1622.60194
AFFX-SNP_10047363 BB 308.29799 788.33384
AFFX-SNP_10047841 AB 898.03389 817.39441
AFFX-SNP_10049334 AB 1726.88965 1310.35894
AFFX-SNP_10052664 BB 309.02089 1043.84560
AFFX-SNP_10057887 AB 591.97652 703.32403
AFFX-SNP_10064911 AA 876.67145 298.26848

Total number of rows: 909622

Table truncated, full table size 33736 Kbytes.

Supplementary file Size Download File type/resource
GSM617689_OR1376.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM617689_OR1376.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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