NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1637396 Query DataSets for GSM1637396
Status Public on Feb 01, 2016
Title blood-Control_5596
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 0.000960 BB 873.545959 4801.273926
SNP_A-1967418 BB 0.002624 BB 334.068268 839.574280
SNP_A-1969580 BB 0.003957 BB 1056.441406 4343.663086
SNP_A-4263484 BB 0.003080 BB 609.024658 2030.582275
SNP_A-1978185 AA 0.001706 AA 1511.333740 483.089691
SNP_A-4264431 AA 0.005903 AA 2322.799072 489.718933
SNP_A-1980898 BB 0.000701 BB 356.514740 912.161926
SNP_A-1983139 AA 0.004344 AA 3285.492920 741.878479
SNP_A-4265735 AA 0.000045 AA 2060.860596 651.533386
SNP_A-1995832 NC 0.333663 AA 1874.758423 793.380920
SNP_A-1995893 AA 0.032724 AA 1750.522461 1039.542236
SNP_A-1997689 BB 0.003954 BB 899.680664 4403.400879
SNP_A-1997709 AA 0.005746 AA 1294.428833 263.939819
SNP_A-1997896 AA 0.004056 AA 1463.806030 701.759644
SNP_A-1997922 AA 0.008759 AA 839.574280 416.424866
SNP_A-2000230 AA 0.004319 AA 2591.794189 1527.080200
SNP_A-2000332 AA 0.003191 AA 3088.363281 933.101440
SNP_A-2000337 AA 0.009203 AA 1704.882812 472.455353
SNP_A-2000342 AA 0.011040 AA 4109.353027 1128.998291
SNP_A-4268173 AA 0.002362 AA 1356.638184 321.557037

Total number of rows: 909622

Table truncated, full table size 46152 Kbytes.




Supplementary file Size Download File type/resource
GSM1637396_5596_GenomeWideSNP_6_.CEL.gz 26.3 Mb (ftp)(http) CEL
GSM1637396_5596_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap