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Sample GSM1636608 Query DataSets for GSM1636608
Status Public on Feb 01, 2016
Title blood-MTC_7660
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 0.007363 AB 2194.160156 2256.600830
SNP_A-1967418 NC 0.672629 AB 371.993011 478.914307
SNP_A-1969580 BB 0.001823 BB 1203.156738 4281.551270
SNP_A-4263484 BB 0.001504 BB 614.752563 1942.430664
SNP_A-1978185 AA 0.005170 AA 1977.667725 403.750977
SNP_A-4264431 AA 0.002202 AA 2007.606934 519.693542
SNP_A-1980898 BB 0.003861 BB 369.723724 832.583252
SNP_A-1983139 AA 0.002381 AA 3268.400879 911.265137
SNP_A-4265735 AA 0.007549 AA 1978.767334 860.678711
SNP_A-1995832 AB 0.001085 AB 1562.807007 1361.490845
SNP_A-1995893 AB 0.000732 AB 1599.416016 1762.635864
SNP_A-1997689 BB 0.005117 BB 648.338867 2785.737305
SNP_A-1997709 AA 0.004423 AA 1660.554688 289.182739
SNP_A-1997896 AA 0.008760 AA 1698.191895 706.668030
SNP_A-1997922 AB 0.034223 AB 386.591187 414.680023
SNP_A-2000230 AA 0.001751 AA 2250.024902 1141.378662
SNP_A-2000332 AA 0.004467 AA 4020.682373 957.194824
SNP_A-2000337 AA 0.013320 AA 904.404541 347.572205
SNP_A-2000342 AA 0.007142 AA 2904.873535 1139.490601
SNP_A-4268173 AB 0.010078 AB 1270.505859 1217.909668

Total number of rows: 909622

Table truncated, full table size 46159 Kbytes.




Supplementary file Size Download File type/resource
GSM1636608_7660_GenomeWideSNP_6_.CEL.gz 27.8 Mb (ftp)(http) CEL
GSM1636608_7660_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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