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Sample GSM617669 Query DataSets for GSM617669
Status Public on Sep 01, 2011
Title OSCC tumor_OR0989
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 AB 796.21125 1609.13880
AFFX-SNP_10009702 AB 726.77784 580.13391
AFFX-SNP_10015773 AA 2085.74655 1017.02864
AFFX-SNP_10021569 AA 785.91815 397.74491
AFFX-SNP_10026879 BB 615.83942 1762.25069
AFFX-SNP_10029725 AB 661.69789 500.68844
AFFX-SNP_10034687 NoCall 857.38534 1143.61546
AFFX-SNP_10036267 BB 342.29036 890.77510
AFFX-SNP_10037362 BB 890.53798 3667.41815
AFFX-SNP_10037636 BB 239.35848 896.97864
AFFX-SNP_10039349 AB 955.63757 820.13383
AFFX-SNP_10039442 AA 1511.55801 193.39301
AFFX-SNP_10039933 BB 698.79128 1886.32140
AFFX-SNP_10046830 AB 837.00209 1263.80291
AFFX-SNP_10047363 AB 562.06434 440.03051
AFFX-SNP_10047841 AB 768.22800 679.18438
AFFX-SNP_10049334 AA 2601.51621 564.16791
AFFX-SNP_10052664 BB 283.99369 1122.92348
AFFX-SNP_10057887 AB 558.75262 573.93283
AFFX-SNP_10064911 AB 793.01437 763.77276

Total number of rows: 909622

Table truncated, full table size 33722 Kbytes.

Supplementary file Size Download File type/resource
GSM617669_OR0989.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM617669_OR0989.birdseed.chp.gz 13.0 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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