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Sample GSM1636618 Query DataSets for GSM1636618
Status Public on Feb 01, 2016
Title blood-MTC_5877
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 0.006025 AB 4014.842285 3254.704834
SNP_A-1967418 BB 0.001269 BB 348.519928 724.348450
SNP_A-1969580 BB 0.008875 BB 718.189392 3120.689941
SNP_A-4263484 BB 0.000527 BB 607.273804 1781.833130
SNP_A-1978185 AA 0.006132 AA 2131.424561 448.855560
SNP_A-4264431 AA 0.005893 AA 2034.229248 336.014343
SNP_A-1980898 BB 0.001457 BB 375.224152 950.722778
SNP_A-1983139 AA 0.004409 AA 2760.027100 878.476501
SNP_A-4265735 BB 0.001691 BB 697.510742 1810.139771
SNP_A-1995832 AA 0.002849 AA 2357.600830 425.040985
SNP_A-1995893 AA 0.001635 AA 2557.781006 1049.702148
SNP_A-1997689 BB 0.001876 BB 778.148499 3186.400391
SNP_A-1997709 AA 0.003986 AA 2312.300537 389.430115
SNP_A-1997896 AA 0.002402 AA 1354.739624 510.484406
SNP_A-1997922 AA 0.008581 AA 959.834778 284.063232
SNP_A-2000230 AA 0.024004 AA 3182.921875 1412.375854
SNP_A-2000332 AB 0.003442 AB 2847.937988 2961.225098
SNP_A-2000337 AA 0.002821 AA 1213.222046 379.340057
SNP_A-2000342 AA 0.006094 AA 3880.639160 905.620728
SNP_A-4268173 AA 0.001063 AA 1458.569580 320.382843

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM1636618_5877_GenomeWideSNP_6_.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM1636618_5877_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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