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Sample GSM397744 Query DataSets for GSM397744
Status Public on Jul 31, 2010
Title Brain-MND-1665-rep1
Sample type genomic
Source name MND Brain (Brodmann area 46)
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 Brain (Brodmann area 46)
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 AB 0.007741 AB 3447.207764 3757.045898
SNP_A-1967418 BB 0.002209 BB 288.403809 719.049805
SNP_A-1969580 BB 0.006750 BB 1159.307495 3489.157227
SNP_A-4263484 AB 0.005387 AB 1775.041626 1492.697510
SNP_A-1978185 AA 0.002905 AA 1579.202026 378.847076
SNP_A-4264431 AA 0.003502 AA 1583.940796 330.946014
SNP_A-1980898 AB 0.000886 AB 572.030212 504.036530
SNP_A-1983139 AA 0.006074 AA 4199.224609 1265.456787
SNP_A-4265735 AA 0.003248 AA 2508.459717 539.429504
SNP_A-1995832 AB 0.002650 AB 2155.910645 1581.606323
SNP_A-1995893 AB 0.001176 AB 1972.250244 2111.977783
SNP_A-1997689 BB 0.010048 BB 989.878296 4459.401855
SNP_A-1997709 AA 0.004158 AA 2784.810791 304.525909
SNP_A-1997896 AA 0.004750 AA 1168.766235 558.525574
SNP_A-1997922 AB 0.001938 AB 798.973511 641.547791
SNP_A-2000230 AA 0.012139 AA 2241.420654 1251.406128
SNP_A-2000332 AB 0.008282 AB 2473.046631 2668.138672
SNP_A-2000337 AA 0.001280 AA 1872.578369 293.812439
SNP_A-2000342 AA 0.001072 AA 4309.432129 1097.604126
SNP_A-4268173 AA 0.003530 AA 1198.056641 267.120575

Total number of rows: 909622

Table truncated, full table size 46128 Kbytes.

Supplementary file Size Download File type/resource
GSM397744.CEL.gz 30.5 Mb (ftp)(http) CEL
GSM397744.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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