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Sample GSM397689 Query DataSets for GSM397689
Status Public on Jul 31, 2010
Title Blood-MND-0844-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 0.004743 BB 557.888733 3818.636719
SNP_A-1967418 BB 0.003643 BB 310.059906 757.168945
SNP_A-1969580 BB 0.000055 BB 1141.795410 4061.176758
SNP_A-4263484 AA 0.002819 AA 2665.949463 308.806030
SNP_A-1978185 AA 0.006443 AA 1743.770142 330.240356
SNP_A-4264431 BB 0.005358 BB 445.612030 1814.646484
SNP_A-1980898 BB 0.005406 BB 287.508057 1052.735352
SNP_A-1983139 AA 0.037090 AA 2431.613037 450.523621
SNP_A-4265735 AA 0.001921 AA 2694.558350 467.646698
SNP_A-1995832 AB 0.008755 AB 1427.531006 898.505615
SNP_A-1995893 AB 0.001462 AB 1832.039551 2127.009033
SNP_A-1997689 BB 0.005686 BB 540.529480 3661.147949
SNP_A-1997709 AA 0.003377 AA 1885.322510 302.568573
SNP_A-1997896 AB 0.011264 AB 1235.786743 2149.125732
SNP_A-1997922 AA 0.014901 AA 1474.659546 269.894958
SNP_A-2000230 AA 0.008481 AA 3277.932129 1269.706421
SNP_A-2000332 AB 0.002115 AB 2956.931396 3251.256348
SNP_A-2000337 AA 0.002642 AA 1980.539795 263.573792
SNP_A-2000342 AA 0.002058 AA 4459.804199 1077.587769
SNP_A-4268173 AB 0.010113 AB 1183.824707 918.689636

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM397689.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM397689.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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