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Sample GSM617757 Query DataSets for GSM617757
Status Public on Sep 01, 2011
Title OSCC tumor_OR4043
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 1180.38016 228.34800
AFFX-SNP_10009702 AA 1115.76527 247.76073
AFFX-SNP_10015773 AA 1623.07661 936.39012
AFFX-SNP_10021569 AA 632.59259 452.65785
AFFX-SNP_10026879 AB 1482.54742 1362.63242
AFFX-SNP_10029725 NoCall 425.77624 472.73090
AFFX-SNP_10034687 AA 914.28733 407.97462
AFFX-SNP_10036267 AA 670.02792 354.64944
AFFX-SNP_10037362 AB 2598.27073 2290.42940
AFFX-SNP_10037636 BB 200.45797 918.08476
AFFX-SNP_10039349 AB 1083.66055 742.03367
AFFX-SNP_10039442 AA 1572.60750 179.45275
AFFX-SNP_10039933 BB 743.35747 1845.11730
AFFX-SNP_10046830 BB 287.55636 1657.01635
AFFX-SNP_10047363 AB 534.06636 325.67278
AFFX-SNP_10047841 AA 1331.52745 386.83776
AFFX-SNP_10049334 AB 1236.69691 1457.35312
AFFX-SNP_10052664 BB 281.62036 972.51042
AFFX-SNP_10057887 BB 273.97009 663.00619
AFFX-SNP_10064911 AA 848.05779 261.06291

Total number of rows: 909622

Table truncated, full table size 33750 Kbytes.

Supplementary file Size Download File type/resource
GSM617757_OR4043.CEL.gz 32.4 Mb (ftp)(http) CEL
GSM617757_OR4043.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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