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Sample GSM397779 Query DataSets for GSM397779
Status Public on Jul 31, 2010
Title Brain-PD-1938-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: F
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 0.010019 BB 995.147156 4870.066895
SNP_A-1967418 BB 0.014406 BB 297.260529 1018.138855
SNP_A-1969580 BB 0.004065 BB 1361.717285 4378.240234
SNP_A-4263484 AA 0.019088 AA 4035.040039 541.792725
SNP_A-1978185 AA 0.000899 AA 1246.700928 351.026428
SNP_A-4264431 AB 0.001976 AB 1313.984009 1013.116333
SNP_A-1980898 BB 0.002185 BB 222.757339 702.070557
SNP_A-1983139 AA 0.010757 AA 4747.480957 1623.464600
SNP_A-4265735 AB 0.005402 AB 2267.854248 2184.117188
SNP_A-1995832 AA 0.034070 AA 4168.760254 487.368988
SNP_A-1995893 AA 0.006331 AA 3706.979492 1423.884766
SNP_A-1997689 BB 0.004628 BB 752.319336 4445.338867
SNP_A-1997709 AA 0.018062 AA 4047.000000 546.423035
SNP_A-1997896 AA 0.002490 AA 1302.491577 561.132141
SNP_A-1997922 AA 0.000871 AA 1032.523682 226.757889
SNP_A-2000230 AA 0.002084 AA 2890.871094 1005.661682
SNP_A-2000332 AB 0.003480 AB 2987.282715 2829.397705
SNP_A-2000337 AA 0.003096 AA 2006.135742 296.281616
SNP_A-2000342 AA 0.003852 AA 4238.872559 1207.171875
SNP_A-4268173 AA 0.000694 AA 1380.453735 265.147858

Total number of rows: 909622

Table truncated, full table size 46119 Kbytes.

Supplementary file Size Download File type/resource
GSM397779.CEL.gz 30.3 Mb (ftp)(http) CEL
GSM397779.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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