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Sample GSM397680 Query DataSets for GSM397680
Status Public on Jul 31, 2010
Title Brain-MND-0539-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 0.000819 AB 2726.881836 3009.154297
SNP_A-1967418 BB 0.001214 BB 242.454681 721.422302
SNP_A-1969580 BB 0.010395 BB 1531.362915 4449.241211
SNP_A-4263484 AA 0.003029 AA 2900.905518 455.781281
SNP_A-1978185 AA 0.006903 AA 794.497498 234.575302
SNP_A-4264431 AA 0.002797 AA 1558.836914 290.688690
SNP_A-1980898 AB 0.004251 AB 495.228271 403.791443
SNP_A-1983139 AA 0.000932 AA 4628.561523 1087.812866
SNP_A-4265735 AB 0.000797 AB 1828.534912 1871.800659
SNP_A-1995832 AB 0.002753 AB 1599.523804 1285.639526
SNP_A-1995893 AB 0.007559 AB 2013.417847 1868.730347
SNP_A-1997689 BB 0.008839 BB 655.465210 3183.132568
SNP_A-1997709 AA 0.003911 AA 2904.862549 413.749847
SNP_A-1997896 AA 0.006429 AA 1060.441040 522.535034
SNP_A-1997922 AB 0.009249 AB 490.912720 507.209686
SNP_A-2000230 AA 0.004313 AA 2327.951904 969.516418
SNP_A-2000332 AA 0.020645 AA 4932.147949 846.304199
SNP_A-2000337 AA 0.005186 AA 2073.666504 242.454681
SNP_A-2000342 AA 0.008391 AA 3532.625244 900.428589
SNP_A-4268173 AA 0.010074 AA 838.421143 171.358032

Total number of rows: 909622

Table truncated, full table size 46124 Kbytes.

Supplementary file Size Download File type/resource
GSM397680.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM397680.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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