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Sample GSM1637316 Query DataSets for GSM1637316
Status Public on Feb 01, 2016
Title blood-PTC_E11039
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 AB 0.002450 AB 3144.463623 2732.493164
SNP_A-1967418 AB 0.005102 AB 614.432617 677.727661
SNP_A-1969580 BB 0.008150 BB 928.582397 2735.008301
SNP_A-4263484 BB 0.010476 BB 733.771606 2532.462891
SNP_A-1978185 AA 0.019848 AA 2609.687500 582.776855
SNP_A-4264431 AB 0.006505 AB 1407.587402 1281.857178
SNP_A-1980898 BB 0.013254 BB 299.805054 1248.343140
SNP_A-1983139 AA 0.001851 AA 3013.208740 835.642944
SNP_A-4265735 AA 0.006521 AA 3401.607422 839.490723
SNP_A-1995832 BB 0.036873 BB 1157.589844 1790.696899
SNP_A-1995893 BB 0.011326 BB 659.413940 3200.307129
SNP_A-1997689 BB 0.004171 BB 701.721008 4176.305176
SNP_A-1997709 AA 0.002112 AA 1494.269287 299.805054
SNP_A-1997896 AA 0.011085 AA 1793.180054 795.350037
SNP_A-1997922 BB 0.003749 BB 598.618103 1073.802734
SNP_A-2000230 NC 0.431582 AB 2546.769287 2040.860352
SNP_A-2000332 BB 0.025689 BB 2127.511963 4962.070801
SNP_A-2000337 AA 0.001718 AA 1403.671387 435.856415
SNP_A-2000342 AA 0.024156 AA 4492.521484 1595.467407
SNP_A-4268173 AA 0.010469 AA 1941.461060 478.945923

Total number of rows: 909622

Table truncated, full table size 46148 Kbytes.




Supplementary file Size Download File type/resource
GSM1637316_E11039_GenomeWideSNP_6_.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM1637316_E11039_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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