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Sample GSM1636631 Query DataSets for GSM1636631
Status Public on Feb 01, 2016
Title blood-MTC_4487
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 0.002850 BB 795.227966 4122.489258
SNP_A-1967418 BB 0.006913 BB 260.509216 749.745239
SNP_A-1969580 BB 0.005998 BB 1377.924683 4720.809082
SNP_A-4263484 BB 0.002085 BB 543.866577 1614.655762
SNP_A-1978185 AA 0.003547 AA 1700.414307 374.354553
SNP_A-4264431 AA 0.002071 AA 1900.423096 379.397095
SNP_A-1980898 BB 0.001735 BB 367.435120 889.398193
SNP_A-1983139 AA 0.002686 AA 3277.497559 928.502991
SNP_A-4265735 AA 0.003349 AA 1946.877808 483.797455
SNP_A-1995832 AB 0.002672 AB 1402.614380 1342.456177
SNP_A-1995893 AB 0.002713 AB 1590.123413 1636.823486
SNP_A-1997689 BB 0.004382 BB 624.499939 3753.515625
SNP_A-1997709 AA 0.006706 AA 1975.301270 295.677643
SNP_A-1997896 AA 0.008629 AA 1398.803345 403.242035
SNP_A-1997922 AB 0.003973 AB 508.891205 548.174927
SNP_A-2000230 AA 0.007196 AA 2058.376709 817.933350
SNP_A-2000332 AA 0.002940 AA 3850.370850 927.775757
SNP_A-2000337 AA 0.005966 AA 1286.625122 279.834717
SNP_A-2000342 AA 0.000325 AA 3253.136475 956.469543
SNP_A-4268173 AA 0.005595 AA 1889.442383 317.200745

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM1636631_4487_GenomeWideSNP_6_.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM1636631_4487_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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