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Sample GSM397825 Query DataSets for GSM397825
Status Public on Jul 31, 2010
Title Blood-MND-1910-rep1
Sample type genomic
 
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 10 / Child
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 AB 0.002262 AB 2849.317383 3319.255371
SNP_A-1967418 BB 0.005063 BB 239.670929 838.979187
SNP_A-1969580 BB 0.001858 BB 1019.389709 3808.895508
SNP_A-4263484 BB 0.005265 BB 473.034760 2272.272461
SNP_A-1978185 AA 0.000294 AA 1268.995239 331.885864
SNP_A-4264431 AA 0.027128 AA 2618.159424 231.723312
SNP_A-1980898 AB 0.028158 AB 907.037659 661.731445
SNP_A-1983139 AA 0.001921 AA 4355.160645 1117.874878
SNP_A-4265735 AA 0.009890 AA 2221.403076 513.713928
SNP_A-1995832 AB 0.004536 AB 2142.548584 1402.020508
SNP_A-1995893 AB 0.009624 AB 2162.927246 2742.187500
SNP_A-1997689 BB 0.008509 BB 701.187866 4627.873047
SNP_A-1997709 AA 0.002658 AA 1841.812866 271.984985
SNP_A-1997896 AB 0.017355 AB 1377.758667 2245.437256
SNP_A-1997922 AA 0.016412 AA 1494.629883 265.897369
SNP_A-2000230 AA 0.013063 AA 2280.822266 1289.305664
SNP_A-2000332 AB 0.007376 AB 2598.899170 2610.990723
SNP_A-2000337 AA 0.000524 AA 1741.205078 279.788239
SNP_A-2000342 AA 0.006179 AA 4572.187500 928.613770
SNP_A-4268173 AA 0.007977 AA 1719.843872 247.607880

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.




Supplementary file Size Download File type/resource
GSM397825.CEL.gz 30.2 Mb (ftp)(http) CEL
GSM397825.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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