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Sample GSM1636648 Query DataSets for GSM1636648
Status Public on Feb 01, 2016
Title blood-MTC_3122
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 0.004834 BB 741.864502 3782.777100
SNP_A-1967418 AB 0.009973 AB 732.687439 654.932129
SNP_A-1969580 BB 0.004173 BB 1059.925537 4369.975586
SNP_A-4263484 AB 0.008280 AB 1359.630859 790.606018
SNP_A-1978185 AA 0.001640 AA 1785.223022 453.304260
SNP_A-4264431 AB 0.001331 AB 1346.313843 1008.238953
SNP_A-1980898 AA 0.005641 AA 1234.513062 281.545563
SNP_A-1983139 AA 0.002013 AA 2767.078613 799.547729
SNP_A-4265735 AB 0.018244 AB 777.594910 735.838440
SNP_A-1995832 BB 0.008804 BB 354.193512 1769.172363
SNP_A-1995893 BB 0.004581 BB 564.149719 2198.902100
SNP_A-1997689 BB 0.007640 BB 521.700684 3338.639160
SNP_A-1997709 AA 0.014013 AA 2336.855713 290.718903
SNP_A-1997896 BB 0.001832 BB 521.700684 2192.901123
SNP_A-1997922 AA 0.001763 AA 761.664673 336.732483
SNP_A-2000230 AA 0.018782 AA 1666.937622 846.494873
SNP_A-2000332 AB 0.001904 AB 2608.688721 2537.322998
SNP_A-2000337 AA 0.005079 AA 1369.594360 284.874664
SNP_A-2000342 AA 0.028392 AA 2783.571289 361.389679
SNP_A-4268173 AA 0.002073 AA 1413.299805 266.763428

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.




Supplementary file Size Download File type/resource
GSM1636648_3122_GenomeWideSNP_6_.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM1636648_3122_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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