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Sample GSM617678 Query DataSets for GSM617678
Status Public on Sep 01, 2011
Title OSCC tumor_OR1260
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 1143.88086 231.02749
AFFX-SNP_10009702 AA 1259.13200 303.18462
AFFX-SNP_10015773 AA 1973.74559 1004.95273
AFFX-SNP_10021569 AA 678.87839 352.14545
AFFX-SNP_10026879 BB 674.26391 1776.37051
AFFX-SNP_10029725 NoCall 703.10341 401.07421
AFFX-SNP_10034687 AA 876.43046 373.11306
AFFX-SNP_10036267 AB 531.59662 574.87302
AFFX-SNP_10037362 BB 1162.28945 4757.66786
AFFX-SNP_10037636 BB 220.94806 995.06831
AFFX-SNP_10039349 BB 330.51693 1070.01302
AFFX-SNP_10039442 AA 1508.40240 272.97290
AFFX-SNP_10039933 BB 845.23112 1992.29491
AFFX-SNP_10046830 BB 264.96168 1863.63423
AFFX-SNP_10047363 AB 652.05601 452.80307
AFFX-SNP_10047841 AB 980.69153 821.49653
AFFX-SNP_10049334 BB 433.33694 1970.55457
AFFX-SNP_10052664 BB 282.35118 951.63430
AFFX-SNP_10057887 AB 511.48376 724.03245
AFFX-SNP_10064911 AB 800.88658 717.01491

Total number of rows: 909622

Table truncated, full table size 33753 Kbytes.

Supplementary file Size Download File type/resource
GSM617678_OR1260.CEL.gz 32.6 Mb (ftp)(http) CEL
GSM617678_OR1260.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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