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Sample GSM397715 Query DataSets for GSM397715
Status Public on Jul 31, 2010
Title Brain-MND-1041-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 BB 0.004049 BB 776.182190 5220.085449
SNP_A-1967418 BB 0.006085 BB 333.648651 813.943542
SNP_A-1969580 BB 0.005253 BB 1135.330444 3541.572266
SNP_A-4263484 AB 0.001231 AB 1931.771729 1324.968872
SNP_A-1978185 AA 0.001889 AA 1122.487427 332.425415
SNP_A-4264431 AA 0.004591 AA 1442.521973 276.194366
SNP_A-1980898 BB 0.003188 BB 190.531113 805.299072
SNP_A-1983139 AA 0.002476 AA 4901.373047 1386.938354
SNP_A-4265735 AA 0.002729 AA 3103.599609 700.818604
SNP_A-1995832 AB 0.012497 AB 2523.255371 2099.028076
SNP_A-1995893 AB 0.002199 AB 2170.233643 2404.836914
SNP_A-1997689 BB 0.000644 BB 709.194397 3856.454346
SNP_A-1997709 AA 0.004533 AA 2954.412598 331.169586
SNP_A-1997896 AB 0.003342 AB 963.647888 1300.132812
SNP_A-1997922 AA 0.022668 AA 690.533875 205.379395
SNP_A-2000230 AA 0.007668 AA 2142.496826 956.876404
SNP_A-2000332 AA 0.003758 AA 4279.735840 839.668274
SNP_A-2000337 AA 0.001403 AA 1878.695801 259.684845
SNP_A-2000342 AA 0.005732 AA 3720.401855 1043.501465
SNP_A-4268173 AA 0.008928 AA 1263.086182 347.521149

Total number of rows: 909622

Table truncated, full table size 46126 Kbytes.

Supplementary file Size Download File type/resource
GSM397715.CEL.gz 30.5 Mb (ftp)(http) CEL
GSM397715.CHP.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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