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Sample GSM1636609 Query DataSets for GSM1636609
Status Public on Feb 01, 2016
Title blood-MTC_7654
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 AB 0.001238 AB 3167.537842 3310.339111
SNP_A-1967418 AB 0.008391 AB 696.715698 560.862000
SNP_A-1969580 BB 0.005187 BB 883.340149 3992.049316
SNP_A-4263484 AB 0.003457 AB 1326.808838 1068.342529
SNP_A-1978185 AA 0.002272 AA 1556.023438 383.826294
SNP_A-4264431 AA 0.009148 AA 2372.787598 425.408386
SNP_A-1980898 BB 0.003155 BB 317.164185 998.246338
SNP_A-1983139 AA 0.003776 AA 2612.147217 591.703979
SNP_A-4265735 AB 0.002263 AB 1293.942139 1240.323853
SNP_A-1995832 AB 0.007784 AB 1842.018066 1773.668823
SNP_A-1995893 AB 0.004870 AB 1832.968384 1999.357056
SNP_A-1997689 BB 0.003632 BB 640.802490 3177.579346
SNP_A-1997709 AA 0.004736 AA 2024.646240 320.171967
SNP_A-1997896 AA 0.008821 AA 1730.180176 634.134644
SNP_A-1997922 AB 0.008552 AB 448.794037 544.538025
SNP_A-2000230 AA 0.010611 AA 2205.621826 704.030945
SNP_A-2000332 AA 0.003848 AA 3717.486328 826.456909
SNP_A-2000337 AA 0.000495 AA 1356.217163 382.125427
SNP_A-2000342 AA 0.000445 AA 3242.078613 976.523621
SNP_A-4268173 AB 0.003488 AB 1187.013550 949.815674

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM1636609_7654_GenomeWideSNP_6_.CEL.gz 28.4 Mb (ftp)(http) CEL
GSM1636609_7654_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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