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Sample GSM1636663 Query DataSets for GSM1636663
Status Public on Feb 01, 2016
Title blood-MTC_1688R
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 0.075335 BB 1350.045532 3348.823242
SNP_A-1967418 AB 0.002730 AB 549.873657 481.729431
SNP_A-1969580 BB 0.009188 BB 1487.633057 4904.524414
SNP_A-4263484 BB 0.006329 BB 466.970856 1381.362671
SNP_A-1978185 AA 0.008087 AA 1633.755737 306.500702
SNP_A-4264431 AA 0.004656 AA 2254.212158 537.597717
SNP_A-1980898 BB 0.020276 BB 319.467377 1216.189331
SNP_A-1983139 AA 0.001949 AA 3110.761230 748.455933
SNP_A-4265735 AB 0.007826 AB 1706.821655 1315.982300
SNP_A-1995832 AA 0.004468 AA 2590.317139 844.505981
SNP_A-1995893 AA 0.002886 AA 2598.504395 1016.045471
SNP_A-1997689 BB 0.007123 BB 578.374146 2711.427734
SNP_A-1997709 AA 0.006022 AA 1253.030762 381.542511
SNP_A-1997896 AB 0.010734 AB 1391.803711 1667.069336
SNP_A-1997922 AA 0.027766 AA 460.482361 221.660126
SNP_A-2000230 AA 0.005131 AA 1986.604736 1295.182861
SNP_A-2000332 AB 0.011280 AB 3067.354248 3290.294922
SNP_A-2000337 AA 0.011783 AA 937.013977 404.761078
SNP_A-2000342 AA 0.003999 AA 2858.473877 911.067383
SNP_A-4268173 AA 0.014908 AA 2286.944824 381.542511

Total number of rows: 909622

Table truncated, full table size 46161 Kbytes.




Supplementary file Size Download File type/resource
GSM1636663_1688R_GenomeWideSNP_6_.CEL.gz 27.1 Mb (ftp)(http) CEL
GSM1636663_1688R_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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