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Sample GSM1636642 Query DataSets for GSM1636642
Status Public on Feb 01, 2016
Title blood-MTC_3550R
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 AA 0.010745 AA 4043.631348 1243.822998
SNP_A-1967418 BB 0.001053 BB 328.743866 783.713928
SNP_A-1969580 BB 0.016953 BB 1564.697388 4048.989014
SNP_A-4263484 BB 0.001542 BB 612.901489 1943.679077
SNP_A-1978185 AB 0.010017 AB 1249.970703 1200.322266
SNP_A-4264431 AB 0.001850 AB 1208.896362 849.014282
SNP_A-1980898 BB 0.000445 BB 348.933594 911.145325
SNP_A-1983139 AA 0.007715 AA 3328.498047 1083.222168
SNP_A-4265735 AA 0.003879 AA 1824.919678 717.384644
SNP_A-1995832 AA 0.007185 AA 2869.496094 671.638977
SNP_A-1995893 AA 0.004478 AA 2423.367188 1258.002197
SNP_A-1997689 BB 0.003955 BB 944.946106 3375.495117
SNP_A-1997709 AA 0.037193 AA 3189.146484 619.231506
SNP_A-1997896 AA 0.002160 AA 1426.666016 654.104736
SNP_A-1997922 AA 0.012357 AA 599.223328 287.118988
SNP_A-2000230 AA 0.001035 AA 2162.045898 1251.751587
SNP_A-2000332 AA 0.002736 AA 3146.306641 975.651245
SNP_A-2000337 AA 0.007062 AA 1673.499634 452.852722
SNP_A-2000342 AA 0.008889 AA 2945.643555 1182.502563
SNP_A-4268173 AB 0.003930 AB 990.689514 691.642944

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.




Supplementary file Size Download File type/resource
GSM1636642_3550R_GenomeWideSNP_6_.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM1636642_3550R_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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