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Sample GSM617668 Query DataSets for GSM617668
Status Public on Sep 01, 2011
Title OSCC tumor_OR0950
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 1015.67522 192.65702
AFFX-SNP_10009702 AB 821.00631 604.43787
AFFX-SNP_10015773 AB 1686.47545 1536.50085
AFFX-SNP_10021569 AA 838.81701 346.71399
AFFX-SNP_10026879 AB 1380.81317 1215.43225
AFFX-SNP_10029725 BB 441.74538 631.28818
AFFX-SNP_10034687 AA 533.16805 392.11080
AFFX-SNP_10036267 BB 356.34334 710.66388
AFFX-SNP_10037362 AB 2508.28819 2416.94549
AFFX-SNP_10037636 BB 196.04853 840.73457
AFFX-SNP_10039349 BB 330.44177 1232.54587
AFFX-SNP_10039442 AA 1306.67691 212.23551
AFFX-SNP_10039933 BB 686.11258 1824.58104
AFFX-SNP_10046830 AB 839.77944 1270.62514
AFFX-SNP_10047363 AB 616.03833 520.13269
AFFX-SNP_10047841 AA 1339.07106 396.04693
AFFX-SNP_10049334 BB 474.75385 1899.99354
AFFX-SNP_10052664 BB 276.47633 1106.67459
AFFX-SNP_10057887 AA 728.36272 452.81834
AFFX-SNP_10064911 AA 999.81548 272.58729

Total number of rows: 909622

Table truncated, full table size 33779 Kbytes.

Supplementary file Size Download File type/resource
GSM617668_OR0950.CEL.gz 34.0 Mb (ftp)(http) CEL
GSM617668_OR0950.birdseed.chp.gz 13.2 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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