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Sample GSM1636599 Query DataSets for GSM1636599
Status Public on Feb 01, 2016
Title blood-MTC_10538
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 0.014990 BB 927.984436 3169.592041
SNP_A-1967418 AB 0.030645 AB 775.130310 595.402344
SNP_A-1969580 BB 0.011374 BB 1542.060425 5013.658203
SNP_A-4263484 AB 0.001498 AB 1611.859985 1125.257568
SNP_A-1978185 AA 0.005412 AA 1818.954346 362.259186
SNP_A-4264431 AA 0.017134 AA 2700.270020 537.796448
SNP_A-1980898 AB 0.021870 AB 980.336975 871.498779
SNP_A-1983139 AA 0.000349 AA 3023.742676 795.656006
SNP_A-4265735 AA 0.002029 AA 2373.763184 738.345764
SNP_A-1995832 AB 0.011864 AB 2127.823486 1839.767822
SNP_A-1995893 AB 0.004708 AB 1816.696533 2024.602539
SNP_A-1997689 BB 0.007836 BB 634.056641 2443.565674
SNP_A-1997709 AA 0.004006 AA 1251.024414 292.030426
SNP_A-1997896 AB 0.040361 AB 1604.916504 2047.185913
SNP_A-1997922 AA 0.009484 AA 622.667114 288.342072
SNP_A-2000230 AA 0.004962 AA 2519.392822 1119.855103
SNP_A-2000332 AB 0.018927 AB 3386.192871 3361.513184
SNP_A-2000337 AA 0.007532 AA 1209.793701 483.185638
SNP_A-2000342 AA 0.007038 AA 2779.540283 1080.154419
SNP_A-4268173 AA 0.020312 AA 2564.437988 566.338867

Total number of rows: 909622

Table truncated, full table size 46164 Kbytes.




Supplementary file Size Download File type/resource
GSM1636599_10538_GenomeWideSNP_6_.CEL.gz 26.7 Mb (ftp)(http) CEL
GSM1636599_10538_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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