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Sample GSM617677 Query DataSets for GSM617677
Status Public on Sep 01, 2011
Title OSCC tumor_OR1240
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 1121.71999 225.04229
AFFX-SNP_10009702 AA 1137.73494 279.21372
AFFX-SNP_10015773 BB 1559.81966 1995.39101
AFFX-SNP_10021569 AA 689.54099 433.39868
AFFX-SNP_10026879 AB 1517.18807 1308.26186
AFFX-SNP_10029725 AB 521.37022 410.88039
AFFX-SNP_10034687 AB 612.29873 886.90076
AFFX-SNP_10036267 AB 461.09580 541.45167
AFFX-SNP_10037362 BB 1048.57931 3577.63051
AFFX-SNP_10037636 BB 198.91910 849.55700
AFFX-SNP_10039349 BB 264.77077 1059.06441
AFFX-SNP_10039442 AA 1510.78049 209.90311
AFFX-SNP_10039933 BB 800.52739 2163.48649
AFFX-SNP_10046830 AB 889.58794 1250.62983
AFFX-SNP_10047363 AB 541.59268 449.94093
AFFX-SNP_10047841 AB 1095.16664 893.71435
AFFX-SNP_10049334 BB 592.80658 1830.51976
AFFX-SNP_10052664 AB 568.63478 568.93413
AFFX-SNP_10057887 AA 677.47831 359.54074
AFFX-SNP_10064911 BB 457.09428 1130.63017

Total number of rows: 909622

Table truncated, full table size 33746 Kbytes.

Supplementary file Size Download File type/resource
GSM617677_OR1240.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM617677_OR1240.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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