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Sample GSM617687 Query DataSets for GSM617687
Status Public on Sep 01, 2011
Title OSCC tumor_OR1343
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 1066.80370 266.56297
AFFX-SNP_10009702 AA 1171.36792 219.17528
AFFX-SNP_10015773 AA 2016.97161 950.62953
AFFX-SNP_10021569 AA 755.30788 400.25532
AFFX-SNP_10026879 AB 1577.19805 1349.90989
AFFX-SNP_10029725 BB 382.69944 661.72110
AFFX-SNP_10034687 AB 577.28119 873.84626
AFFX-SNP_10036267 BB 369.55620 773.24318
AFFX-SNP_10037362 BB 970.94237 3509.67714
AFFX-SNP_10037636 BB 234.54493 812.85297
AFFX-SNP_10039349 AB 779.26411 743.10614
AFFX-SNP_10039442 AA 1660.36322 230.53418
AFFX-SNP_10039933 BB 740.22846 1739.00830
AFFX-SNP_10046830 BB 300.71174 2051.36634
AFFX-SNP_10047363 BB 309.25803 642.90765
AFFX-SNP_10047841 AB 1062.71347 867.91394
AFFX-SNP_10049334 BB 489.04001 1884.89073
AFFX-SNP_10052664 BB 275.12048 1018.40397
AFFX-SNP_10057887 AB 549.12966 680.01180
AFFX-SNP_10064911 BB 536.01520 1223.85244

Total number of rows: 909622

Table truncated, full table size 33741 Kbytes.

Supplementary file Size Download File type/resource
GSM617687_OR1343.CEL.gz 32.5 Mb (ftp)(http) CEL
GSM617687_OR1343.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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