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Sample GSM1637375 Query DataSets for GSM1637375
Status Public on Feb 01, 2016
Title blood-Control_5940
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 0.004950 BB 1127.922363 5867.750000
SNP_A-1967418 AB 0.014575 AB 606.191040 756.649963
SNP_A-1969580 BB 0.003550 BB 925.194580 3425.139160
SNP_A-4263484 BB 0.017584 BB 732.133057 1417.544312
SNP_A-1978185 AA 0.014134 AA 1178.494019 592.798645
SNP_A-4264431 AB 0.001273 AB 1304.764038 1034.622803
SNP_A-1980898 BB 0.001010 BB 367.120758 943.735901
SNP_A-1983139 AA 0.003862 AA 3225.933594 729.674866
SNP_A-4265735 AA 0.017988 AA 3340.651611 947.369690
SNP_A-1995832 AA 0.006811 AA 2859.104736 835.127991
SNP_A-1995893 AA 0.002125 AA 2526.002441 1199.356812
SNP_A-1997689 BB 0.005745 BB 929.806458 2989.303467
SNP_A-1997709 AA 0.006747 AA 2446.709229 462.707672
SNP_A-1997896 AA 0.007433 AA 980.468140 598.487732
SNP_A-1997922 AA 0.014962 AA 646.817871 331.349457
SNP_A-2000230 AA 0.000730 AA 2187.336182 1285.345581
SNP_A-2000332 AB 0.000706 AB 2677.104736 2712.099609
SNP_A-2000337 AA 0.001300 AA 1305.733154 391.479095
SNP_A-2000342 AA 0.004958 AA 2783.339844 948.320374
SNP_A-4268173 AA 0.003612 AA 1240.859619 277.407410

Total number of rows: 909622

Table truncated, full table size 46130 Kbytes.




Supplementary file Size Download File type/resource
GSM1637375_5940_GenomeWideSNP_6_.CEL.gz 26.9 Mb (ftp)(http) CEL
GSM1637375_5940_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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