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Sample GSM1636641 Query DataSets for GSM1636641
Status Public on Feb 01, 2016
Title blood-MTC_3569
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 BB 0.001843 BB 996.333862 5279.784180
SNP_A-1967418 BB 0.016985 BB 315.956329 1015.893005
SNP_A-1969580 BB 0.002521 BB 1038.975342 4155.074219
SNP_A-4263484 BB 0.002290 BB 502.084076 1715.702393
SNP_A-1978185 AA 0.001492 AA 1412.765137 406.122620
SNP_A-4264431 AB 0.002240 AB 1285.766113 1080.585327
SNP_A-1980898 AB 0.002750 AB 690.133301 713.136841
SNP_A-1983139 AA 0.001319 AA 2766.615967 708.355225
SNP_A-4265735 AA 0.000920 AA 2058.421631 601.320435
SNP_A-1995832 AB 0.004836 AB 1920.430054 1543.295532
SNP_A-1995893 AB 0.004866 AB 1703.887939 1635.583984
SNP_A-1997689 BB 0.005495 BB 697.043518 2646.302002
SNP_A-1997709 AA 0.000383 AA 1777.817627 370.881561
SNP_A-1997896 AB 0.002350 AB 1137.273315 1515.832275
SNP_A-1997922 AA 0.001005 AA 832.026184 351.462555
SNP_A-2000230 AA 0.007355 AA 2549.512695 1014.886047
SNP_A-2000332 AB 0.018233 AB 3103.886475 3492.373291
SNP_A-2000337 AA 0.000298 AA 1383.349243 372.569519
SNP_A-2000342 AA 0.003200 AA 3670.059082 927.354431
SNP_A-4268173 AB 0.005559 AB 1211.405029 1095.668945

Total number of rows: 909622

Table truncated, full table size 46143 Kbytes.




Supplementary file Size Download File type/resource
GSM1636641_3569_GenomeWideSNP_6_.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM1636641_3569_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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