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Sample GSM1637326 Query DataSets for GSM1637326
Status Public on Feb 01, 2016
Title blood-PTC_E11205
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: PTC
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 0.006114 AB 2762.735840 2315.912109
SNP_A-1967418 BB 0.007203 BB 273.321869 824.104248
SNP_A-1969580 BB 0.003039 BB 843.271484 3381.932129
SNP_A-4263484 AB 0.002301 AB 1845.297485 1348.618774
SNP_A-1978185 AA 0.009287 AA 2205.519043 564.118286
SNP_A-4264431 AB 0.002971 AB 1430.562988 1157.314819
SNP_A-1980898 AB 0.003448 AB 713.143433 564.118286
SNP_A-1983139 AA 0.004892 AA 2667.802734 829.610535
SNP_A-4265735 AA 0.003504 AA 3009.591553 736.054138
SNP_A-1995832 NC 0.314735 AB 1061.544556 1326.704590
SNP_A-1995893 BB 0.003185 BB 496.225372 2792.307861
SNP_A-1997689 BB 0.000559 BB 840.526855 3752.685791
SNP_A-1997709 AA 0.001741 AA 1406.073364 312.147186
SNP_A-1997896 BB 0.006363 BB 662.149597 2715.421143
SNP_A-1997922 AA 0.010410 AA 772.614380 373.249512
SNP_A-2000230 NC 0.751157 AB 2607.642334 2010.163574
SNP_A-2000332 AB 0.004127 AB 2866.418213 2912.210449
SNP_A-2000337 AA 0.010869 AA 1025.019531 475.769135
SNP_A-2000342 AA 0.008503 AA 4154.917969 1348.618774
SNP_A-4268173 AB 0.002036 AB 909.060730 851.480774

Total number of rows: 909622

Table truncated, full table size 46157 Kbytes.




Supplementary file Size Download File type/resource
GSM1637326_E11205_GenomeWideSNP_6_.CEL.gz 26.3 Mb (ftp)(http) CEL
GSM1637326_E11205_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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