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Sample GSM397777 Query DataSets for GSM397777
Status Public on Jul 31, 2010
Title Brain-MND-1895-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: 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 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 0.012367 AB 1958.026611 2243.448486
SNP_A-1967418 BB 0.006600 BB 235.816055 563.316162
SNP_A-1969580 BB 0.005930 BB 1419.538330 4611.838867
SNP_A-4263484 AB 0.004432 AB 1531.780151 1071.000366
SNP_A-1978185 AA 0.007472 AA 1510.799805 204.523865
SNP_A-4264431 AA 0.003120 AA 1980.938232 264.937134
SNP_A-1980898 BB 0.006076 BB 239.571671 1069.620728
SNP_A-1983139 AA 0.006264 AA 5236.726074 1101.606812
SNP_A-4265735 AB 0.005050 AB 1796.907593 1644.875488
SNP_A-1995832 BB 0.000987 BB 626.290161 2377.487061
SNP_A-1995893 BB 0.005540 BB 310.901398 2523.095215
SNP_A-1997689 BB 0.003412 BB 628.329407 3599.914795
SNP_A-1997709 AA 0.002458 AA 1948.896484 296.789703
SNP_A-1997896 AA 0.001317 AA 1434.984985 499.083527
SNP_A-1997922 BB 0.020869 BB 283.992889 771.393555
SNP_A-2000230 AA 0.018825 AA 2247.787842 593.822693
SNP_A-2000332 AA 0.005434 AA 4469.019043 883.579590
SNP_A-2000337 AA 0.006037 AA 1567.486328 208.472458
SNP_A-2000342 AA 0.003507 AA 4029.218750 873.425110
SNP_A-4268173 AA 0.004951 AA 1509.383667 352.195007

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.

Supplementary file Size Download File type/resource
GSM397777.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM397777.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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