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Sample GSM1637404 Query DataSets for GSM1637404
Status Public on Feb 01, 2016
Title blood-Control_5487
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 0.004705 BB 1060.500977 3915.291992
SNP_A-1967418 BB 0.001960 BB 327.975006 813.496582
SNP_A-1969580 BB 0.005346 BB 1416.510864 4250.148438
SNP_A-4263484 AB 0.006484 AB 1291.286011 845.786499
SNP_A-1978185 AA 0.014807 AA 841.737244 263.740936
SNP_A-4264431 AA 0.003285 AA 2139.099854 439.720428
SNP_A-1980898 NC 0.262007 AB 467.369720 689.901978
SNP_A-1983139 AA 0.002951 AA 2770.349609 628.235901
SNP_A-4265735 AB 0.001270 AB 1527.678467 1462.685791
SNP_A-1995832 AB 0.001127 AB 1571.447632 1368.669312
SNP_A-1995893 AB 0.005229 AB 1312.109741 1616.070923
SNP_A-1997689 BB 0.001272 BB 801.358459 3327.577148
SNP_A-1997709 AA 0.003787 AA 1203.492554 318.951782
SNP_A-1997896 AA 0.012137 AA 1529.764526 825.589966
SNP_A-1997922 AB 0.005094 AB 492.107239 554.731140
SNP_A-2000230 AA 0.027679 AA 1962.426758 1550.614136
SNP_A-2000332 AA 0.004619 AA 3931.784424 878.161621
SNP_A-2000337 AA 0.007627 AA 1492.046631 500.080444
SNP_A-2000342 AA 0.007511 AA 3268.512695 1232.752075
SNP_A-4268173 AA 0.008094 AA 1858.772095 264.587616

Total number of rows: 909622

Table truncated, full table size 46153 Kbytes.




Supplementary file Size Download File type/resource
GSM1637404_5487_GenomeWideSNP_6_.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM1637404_5487_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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