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Sample GSM617675 Query DataSets for GSM617675
Status Public on Sep 01, 2011
Title OSCC tumor_OR1077
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 BB 410.51405 2492.85835
AFFX-SNP_10009702 NoCall 505.58761 652.22743
AFFX-SNP_10015773 AA 1949.70231 1197.81926
AFFX-SNP_10021569 AA 592.41234 405.04041
AFFX-SNP_10026879 BB 730.84188 2127.89394
AFFX-SNP_10029725 AB 531.42713 492.45974
AFFX-SNP_10034687 AA 1007.08655 468.66574
AFFX-SNP_10036267 NoCall 419.30884 648.82027
AFFX-SNP_10037362 BB 1287.49121 4165.96192
AFFX-SNP_10037636 AB 401.93763 488.39080
AFFX-SNP_10039349 AB 821.62156 659.37491
AFFX-SNP_10039442 AA 1734.64094 178.24613
AFFX-SNP_10039933 BB 739.69437 1999.35384
AFFX-SNP_10046830 AB 1012.36017 1052.64557
AFFX-SNP_10047363 BB 339.17372 544.35693
AFFX-SNP_10047841 AB 971.22271 996.85242
AFFX-SNP_10049334 NoCall 2177.46949 769.59673
AFFX-SNP_10052664 BB 312.24470 920.02790
AFFX-SNP_10057887 AA 755.11058 429.96901
AFFX-SNP_10064911 AB 794.09667 808.17447

Total number of rows: 909622

Table truncated, full table size 33821 Kbytes.

Supplementary file Size Download File type/resource
GSM617675_OR1077.CEL.gz 33.1 Mb (ftp)(http) CEL
GSM617675_OR1077.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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