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Sample GSM397699 Query DataSets for GSM397699
Status Public on Jul 31, 2010
Title Blood-MND-0914-rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: F
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
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
SNP_A-2131660 BB 0.001603 BB 632.721863 4240.475098
SNP_A-1967418 BB 0.058980 BB 262.110657 463.893860
SNP_A-1969580 BB 0.006876 BB 839.454712 3385.077637
SNP_A-4263484 AA 0.008544 AA 2268.815918 240.673904
SNP_A-1978185 AA 0.004774 AA 1058.280884 395.774597
SNP_A-4264431 AA 0.002075 AA 1609.903320 282.380157
SNP_A-1980898 AB 0.007957 AB 421.843384 504.547424
SNP_A-1983139 AA 0.003659 AA 4079.604492 973.681458
SNP_A-4265735 AA 0.001239 AA 2676.318848 492.216125
SNP_A-1995832 AA 0.008568 AA 2302.746094 403.180206
SNP_A-1995893 AB 0.005960 AB 1568.167603 2004.763550
SNP_A-1997689 BB 0.007617 BB 558.410400 3340.472900
SNP_A-1997709 AA 0.008840 AA 2130.855713 181.007599
SNP_A-1997896 AA 0.001379 AA 1229.034546 428.064941
SNP_A-1997922 AB 0.006923 AB 568.446167 613.733154
SNP_A-2000230 AA 0.003177 AA 3014.291748 1036.555176
SNP_A-2000332 AB 0.002618 AB 2889.479248 3267.976074
SNP_A-2000337 AA 0.001590 AA 1664.258423 262.110657
SNP_A-2000342 AA 0.008073 AA 3637.970703 805.970581
SNP_A-4268173 AB 0.001591 AB 907.782104 757.847656

Total number of rows: 909622

Table truncated, full table size 46131 Kbytes.

Supplementary file Size Download File type/resource
GSM397699.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM397699.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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