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Sample GSM1636621 Query DataSets for GSM1636621
Status Public on Feb 01, 2016
Title blood-MTC_5419
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: MTC
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 0.000759 BB 920.641541 4586.694336
SNP_A-1967418 BB 0.000843 BB 323.998749 741.745300
SNP_A-1969580 BB 0.003403 BB 1283.656494 4478.968262
SNP_A-4263484 BB 0.002984 BB 510.679443 1557.829834
SNP_A-1978185 AA 0.006648 AA 1865.872559 352.764191
SNP_A-4264431 AA 0.004505 AA 2131.707031 398.268311
SNP_A-1980898 BB 0.001628 BB 338.477264 866.101685
SNP_A-1983139 AA 0.004851 AA 3015.748535 628.218262
SNP_A-4265735 AB 0.002656 AB 1144.446899 1251.478516
SNP_A-1995832 BB 0.000927 BB 722.158325 2050.758545
SNP_A-1995893 BB 0.000575 BB 546.984802 2429.882568
SNP_A-1997689 BB 0.000773 BB 762.631714 3464.884766
SNP_A-1997709 AA 0.001742 AA 1507.390747 359.592072
SNP_A-1997896 BB 0.004071 BB 608.533936 1959.346313
SNP_A-1997922 AA 0.008914 AA 746.248901 373.304352
SNP_A-2000230 AA 0.002098 AA 2139.108643 1120.399292
SNP_A-2000332 AA 0.017720 AA 3817.930176 555.039551
SNP_A-2000337 AA 0.004388 AA 1574.301147 320.346252
SNP_A-2000342 AA 0.002629 AA 3582.869629 1050.052002
SNP_A-4268173 AA 0.000326 AA 1563.726685 350.909271

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.




Supplementary file Size Download File type/resource
GSM1636621_5419_GenomeWideSNP_6_.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM1636621_5419_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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