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Sample GSM1636653 Query DataSets for GSM1636653
Status Public on Feb 01, 2016
Title blood-MTC_2766
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 0.002900 BB 832.108521 4086.022217
SNP_A-1967418 AB 0.004709 AB 523.236511 449.162903
SNP_A-1969580 BB 0.002384 BB 1082.704712 4231.055664
SNP_A-4263484 AB 0.003410 AB 1334.679321 1089.801270
SNP_A-1978185 AA 0.004523 AA 1915.058960 531.134094
SNP_A-4264431 AB 0.002234 AB 1363.784546 928.098694
SNP_A-1980898 BB 0.001584 BB 361.378052 983.871948
SNP_A-1983139 AA 0.002852 AA 2621.509766 753.970642
SNP_A-4265735 AB 0.010932 AB 950.249146 850.109619
SNP_A-1995832 AA 0.016554 AA 1641.969116 376.435974
SNP_A-1995893 AA 0.003350 AA 2616.686523 1009.210327
SNP_A-1997689 BB 0.003610 BB 672.963806 3940.050049
SNP_A-1997709 AA 0.002348 AA 1993.276733 412.341797
SNP_A-1997896 AA 0.004569 AA 1556.020874 549.499268
SNP_A-1997922 AA 0.010771 AA 940.571533 254.640945
SNP_A-2000230 AA 0.043400 AA 1708.852905 1206.788330
SNP_A-2000332 AA 0.000675 AA 3495.010742 1015.420654
SNP_A-2000337 AA 0.005231 AA 1263.387207 292.859039
SNP_A-2000342 AA 0.003727 AA 3564.808350 817.680176
SNP_A-4268173 AB 0.001392 AB 1075.614136 906.032166

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.




Supplementary file Size Download File type/resource
GSM1636653_2766_GenomeWideSNP_6_.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM1636653_2766_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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