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Sample GSM397780 Query DataSets for GSM397780
Status Public on Jul 31, 2010
Title Brain-PD-1939-rep1
Sample type genomic
Source name PD Brain (Brodmann area 46)
Organism Homo sapiens
Characteristics study #: Study 1 (Somatic)
trio #: NA
twin #: NA
twin info: NA
gender: M
phenotype: PD
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 PD 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 0.013621 BB 652.568604 5596.737793
SNP_A-1967418 BB 0.004150 BB 248.395218 836.663391
SNP_A-1969580 BB 0.004801 BB 1370.138672 4591.690918
SNP_A-4263484 BB 0.003273 BB 458.010193 1877.476562
SNP_A-1978185 AA 0.002355 AA 1062.896240 291.773041
SNP_A-4264431 AB 0.003601 AB 1169.162720 796.049683
SNP_A-1980898 AB 0.003765 AB 549.307312 585.183838
SNP_A-1983139 AA 0.002878 AA 4397.856445 932.013245
SNP_A-4265735 AB 0.001460 AB 1742.546997 1786.036499
SNP_A-1995832 BB 0.001630 BB 566.405640 2449.930664
SNP_A-1995893 BB 0.002753 BB 465.081299 2727.960205
SNP_A-1997689 BB 0.001156 BB 692.927002 4031.895264
SNP_A-1997709 AA 0.003412 AA 1719.796753 255.767914
SNP_A-1997896 AA 0.000538 AA 1376.559937 489.046753
SNP_A-1997922 BB 0.004550 BB 433.004211 951.110352
SNP_A-2000230 AA 0.004668 AA 2379.272949 886.162476
SNP_A-2000332 AA 0.006124 AA 3701.940430 741.029236
SNP_A-2000337 AA 0.008055 AA 2218.620117 259.993622
SNP_A-2000342 AA 0.012116 AA 3480.564453 749.282837
SNP_A-4268173 AA 0.000717 AA 1309.218506 220.347076

Total number of rows: 909622

Table truncated, full table size 46128 Kbytes.

Supplementary file Size Download File type/resource
GSM397780.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM397780.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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