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Sample GSM397714 Query DataSets for GSM397714
Status Public on Jul 31, 2010
Title Blood-MND-1041-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 0.001321 BB 755.799255 4655.902344
SNP_A-1967418 BB 0.005271 BB 315.054108 716.040894
SNP_A-1969580 BB 0.001554 BB 1223.330444 4066.677246
SNP_A-4263484 AB 0.004306 AB 1641.319824 1086.530518
SNP_A-1978185 AA 0.000869 AA 1304.243286 363.150360
SNP_A-4264431 AA 0.001606 AA 1742.594971 333.116272
SNP_A-1980898 BB 0.003574 BB 212.643539 934.826721
SNP_A-1983139 AA 0.009532 AA 3647.355225 1002.593628
SNP_A-4265735 AA 0.005460 AA 2479.622559 589.454834
SNP_A-1995832 AB 0.003924 AB 1660.847900 1123.548950
SNP_A-1995893 AB 0.014760 AB 1716.924805 2509.698730
SNP_A-1997689 BB 0.010286 BB 1011.245056 4217.107422
SNP_A-1997709 AA 0.000883 AA 2496.751953 342.906494
SNP_A-1997896 AB 0.002441 AB 924.729614 1345.793213
SNP_A-1997922 AA 0.002607 AA 882.655151 221.150253
SNP_A-2000230 AA 0.013647 AA 2486.607910 1377.453491
SNP_A-2000332 AA 0.005654 AA 3604.827637 863.095154
SNP_A-2000337 AA 0.002999 AA 1946.335083 313.676697
SNP_A-2000342 AA 0.009480 AA 4004.873047 1285.929199
SNP_A-4268173 AA 0.000149 AA 1360.941284 248.634171

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.




Supplementary file Size Download File type/resource
GSM397714.CEL.gz 30.4 Mb (ftp)(http) CEL
GSM397714.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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