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Sample GSM1636652 Query DataSets for GSM1636652
Status Public on Feb 01, 2016
Title blood-MTC_2769
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 0.004396 BB 601.347961 4102.130859
SNP_A-1967418 BB 0.003913 BB 283.402863 730.485779
SNP_A-1969580 BB 0.005029 BB 1271.078979 4665.294434
SNP_A-4263484 AB 0.003374 AB 1351.322388 974.222229
SNP_A-1978185 AA 0.006637 AA 2152.015625 442.569458
SNP_A-4264431 AB 0.004156 AB 1377.842285 1161.088867
SNP_A-1980898 BB 0.002469 BB 387.164368 910.119019
SNP_A-1983139 AA 0.004993 AA 2427.076172 719.617676
SNP_A-4265735 AA 0.014081 AA 1039.712402 396.907257
SNP_A-1995832 AA 0.002870 AA 2036.549683 392.672272
SNP_A-1995893 AA 0.002057 AA 2524.009766 1004.534302
SNP_A-1997689 BB 0.005536 BB 588.743530 3711.533447
SNP_A-1997709 AA 0.003181 AA 2220.250000 414.318329
SNP_A-1997896 AA 0.010532 AA 1689.511963 502.631287
SNP_A-1997922 AA 0.011077 AA 1020.079956 298.506775
SNP_A-2000230 AA 0.004429 AA 2067.017334 964.791016
SNP_A-2000332 AA 0.004893 AA 3545.515381 759.479065
SNP_A-2000337 AA 0.000724 AA 1338.691040 377.689270
SNP_A-2000342 AA 0.010843 AA 4003.298340 764.334595
SNP_A-4268173 AA 0.000745 AA 1650.801025 342.343781

Total number of rows: 909622

Table truncated, full table size 46135 Kbytes.




Supplementary file Size Download File type/resource
GSM1636652_2769_GenomeWideSNP_6_.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM1636652_2769_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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