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Sample GSM1637314 Query DataSets for GSM1637314
Status Public on Feb 01, 2016
Title blood-PTC_E11024b
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: PTC
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 0.003706 BB 661.878662 4084.678467
SNP_A-1967418 AB 0.003713 AB 636.165222 579.650940
SNP_A-1969580 BB 0.002862 BB 1016.077881 4124.859863
SNP_A-4263484 AB 0.026787 AB 2489.350342 1570.385864
SNP_A-1978185 AA 0.003226 AA 1249.771851 372.782745
SNP_A-4264431 AB 0.008128 AB 1655.595947 1301.167725
SNP_A-1980898 BB 0.023919 BB 336.686646 1375.785278
SNP_A-1983139 AA 0.004534 AA 2516.105225 546.451355
SNP_A-4265735 AA 0.047412 AA 4417.198730 632.397705
SNP_A-1995832 AA 0.002955 AA 2012.062134 456.863617
SNP_A-1995893 AA 0.008594 AA 1885.158081 897.998169
SNP_A-1997689 BB 0.013825 BB 638.845032 2544.510986
SNP_A-1997709 AA 0.013306 AA 2126.176025 262.000122
SNP_A-1997896 AA 0.003281 AA 1489.922852 538.043274
SNP_A-1997922 AA 0.008215 AA 830.833984 240.434235
SNP_A-2000230 AA 0.059664 AA 4360.835449 1473.761108
SNP_A-2000332 AB 0.030729 AB 3637.838135 3238.102539
SNP_A-2000337 AA 0.006279 AA 1669.073730 436.092682
SNP_A-2000342 AA 0.014920 AA 4554.647461 876.497131
SNP_A-4268173 AB 0.003735 AB 1125.907227 904.401917

Total number of rows: 909622

Table truncated, full table size 46157 Kbytes.




Supplementary file Size Download File type/resource
GSM1637314_E11024b_GenomeWideSNP_6_.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM1637314_E11024b_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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