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Sample GSM1636659 Query DataSets for GSM1636659
Status Public on Feb 01, 2016
Title blood-MTC_2220R
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: MTC
tissue: peripheral blood
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from peripheral blood using MagNA Pure LC 2.0 System. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer 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 images were obtained using an Affymetrix GeneChip® Scanner 3000.
Data processing CEL files were processed using Affymetrix Power Tools (APT v1.15.0) using Birdseed v2 calling algorithm.
 
Submission date Mar 18, 2015
Last update date Feb 01, 2016
Contact name Joaquin Dopazo
E-mail(s) jdopazo@cipf.es
Organization name Centro de Investigacion Principe Felipe
Department Systems Biology
Street address Eduardo Primo Y├║fera, 3
City Valencia
State/province Valencia
ZIP/Postal code 46012
Country Spain
 
Platform ID GPL6801
Series (1)
GSE67047 Genome-wide association and epistatic studies in sporadic medullary and juvenile papillary thyroid carcinomas

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE
FORCED CALL
SIGNAL A Summarized signal
SIGNAL B Summarized signal

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 NC 0.190059 BB 1222.425537 2898.638428
SNP_A-1967418 BB 0.000887 BB 356.383148 778.394165
SNP_A-1969580 BB 0.009729 BB 1557.649048 4673.729492
SNP_A-4263484 AA 0.000525 AA 2387.765381 486.232605
SNP_A-1978185 AA 0.001886 AA 1765.098022 425.841278
SNP_A-4264431 AB 0.002240 AB 1406.542725 1015.363098
SNP_A-1980898 BB 0.004038 BB 406.508484 906.081543
SNP_A-1983139 AA 0.004082 AA 3275.524414 986.240234
SNP_A-4265735 AB 0.003782 AB 1506.225586 1287.793579
SNP_A-1995832 AB 0.002583 AB 1738.132324 1487.309692
SNP_A-1995893 AB 0.006187 AB 1528.927124 1470.124390
SNP_A-1997689 BB 0.012580 BB 814.752808 2082.385742
SNP_A-1997709 AA 0.006025 AA 1303.102295 389.838654
SNP_A-1997896 AB 0.003726 AB 1067.738281 1622.884644
SNP_A-1997922 AA 0.056466 AA 539.803589 316.884094
SNP_A-2000230 AA 0.001436 AA 2256.747314 1169.378662
SNP_A-2000332 BB 0.004753 BB 1643.443481 4135.064453
SNP_A-2000337 AA 0.012193 AA 935.115234 336.337189
SNP_A-2000342 AA 0.001757 AA 3102.857178 1011.637939
SNP_A-4268173 AA 0.002820 AA 1834.077271 443.909790

Total number of rows: 909622

Table truncated, full table size 46165 Kbytes.




Supplementary file Size Download File type/resource
GSM1636659_2220R_GenomeWideSNP_6_.CEL.gz 27.4 Mb (ftp)(http) CEL
GSM1636659_2220R_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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