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Sample GSM1637376 Query DataSets for GSM1637376
Status Public on Feb 01, 2016
Title blood-Control_5935
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: Control
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 0.025602 BB 1120.495483 7411.882324
SNP_A-1967418 BB 0.005741 BB 396.998932 899.315674
SNP_A-1969580 BB 0.005839 BB 1043.182739 3225.029053
SNP_A-4263484 BB 0.003880 BB 593.892883 1556.695435
SNP_A-1978185 AA 0.001258 AA 1435.440918 456.767853
SNP_A-4264431 BB 0.006377 BB 590.222961 1707.928101
SNP_A-1980898 AB 0.003943 AB 818.812195 620.353027
SNP_A-1983139 AA 0.001374 AA 3177.148193 854.249817
SNP_A-4265735 AA 0.016031 AA 3264.176758 922.163391
SNP_A-1995832 AB 0.008557 AB 2092.811523 1635.524902
SNP_A-1995893 AB 0.009340 AB 1936.414795 2159.980225
SNP_A-1997689 BB 0.004698 BB 923.915833 3117.164307
SNP_A-1997709 AA 0.003314 AA 2001.870605 427.149658
SNP_A-1997896 AA 0.002515 AA 1263.250488 656.322571
SNP_A-1997922 AB 0.006851 AB 647.995911 699.203735
SNP_A-2000230 AA 0.002086 AA 2397.983398 1492.599243
SNP_A-2000332 BB 0.001656 BB 1251.979736 3698.267578
SNP_A-2000337 AA 0.001100 AA 1388.313965 408.488953
SNP_A-2000342 AA 0.000248 AA 3277.034668 976.028320
SNP_A-4268173 AA 0.005485 AA 1146.111450 284.326416

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.




Supplementary file Size Download File type/resource
GSM1637376_5935_GenomeWideSNP_6_.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM1637376_5935_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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