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Sample GSM397712 Query DataSets for GSM397712
Status Public on Jul 31, 2010
Title Blood-MND-1016-rep1
Sample type genomic
 
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
phenotype: MND
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from leukocytes using the phenol chloroform method or Qiamp blood kits (Qiagen Pty Ltd, Doncaster, Vic, Australia), hair using the phenol chloroform method, and from sperm using Pure Sperm 100 kits (Nidacom, Gothenburg, Sweden).
Label biotin
Label protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia), Affymetrix dsDNA terminal label.
 
Hybridization protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Scan protocol According to manufacturer protocol (The Ramaciotti Centre for Gene Function Analysis, Sydney, Australia)
Description Affy 6.0 MND Blood
Data processing Data processed using Affymetrix Command Console software and Affymetrix Genotyping Console 3.0.2 software using the Birdseed version 2 algorithm and default settings.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
 
Submission date Apr 25, 2009
Last update date Jun 26, 2012
Contact name Roger Pamphlett
Organization name University of Sydney
Street address Blackburn Bld
City University of Sydney
ZIP/Postal code 2006
Country Australia
 
Platform ID GPL6801
Series (1)
GSE15826 Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE A value in the range [0,1] with lower values corresponding to greater confidence
FORCED CALL This value is the genotyping call that would be made if the calling algorithm were tuned to the least stringency. Providing this value allows for determining what the calls would have been at a stringency different to that applied to the calls in the second field, without having to re-run the genotyping algorithm
SIGNAL A Summarized signal A
SIGNAL B Summarized signal B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.017356 BB 569.041870 5526.626465
SNP_A-1967418 BB 0.002646 BB 224.938644 717.639343
SNP_A-1969580 BB 0.004963 BB 1094.216309 4472.481934
SNP_A-4263484 BB 0.000175 BB 503.939911 2086.205078
SNP_A-1978185 AA 0.002194 AA 1387.001953 408.912659
SNP_A-4264431 AA 0.006645 AA 2184.559570 266.406555
SNP_A-1980898 BB 0.002330 BB 249.082565 960.874084
SNP_A-1983139 AA 0.001103 AA 4614.003418 1225.139526
SNP_A-4265735 AB 0.000987 AB 1727.730591 1866.912964
SNP_A-1995832 AB 0.000868 AB 1930.721191 1535.982300
SNP_A-1995893 AB 0.001785 AB 2108.059326 2217.990967
SNP_A-1997689 BB 0.002196 BB 634.296143 3838.841797
SNP_A-1997709 AA 0.004439 AA 2512.052490 261.004974
SNP_A-1997896 AA 0.006165 AA 1659.703369 513.124268
SNP_A-1997922 AB 0.001470 AB 669.095276 568.189087
SNP_A-2000230 AA 0.002159 AA 2705.715088 940.383972
SNP_A-2000332 AB 0.009213 AB 3170.775146 2712.924316
SNP_A-2000337 AA 0.007081 AA 1729.871948 187.210678
SNP_A-2000342 AA 0.002927 AA 3908.003418 1044.602661
SNP_A-4268173 AA 0.006453 AA 1586.776123 208.288284

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.




Supplementary file Size Download File type/resource
GSM397712.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM397712.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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