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Sample GSM397820 Query DataSets for GSM397820
Status Public on Jul 31, 2010
Title Blood-MND-1685rep1
Sample type genomic
Source name MND Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 5 / Child
twin #: NA
twin info: NA
gender: F
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 Blood
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 0.005589 AB 2294.987549 2494.738037
SNP_A-1967418 BB 0.005314 BB 200.404861 633.400452
SNP_A-1969580 BB 0.006953 BB 931.966248 4212.682617
SNP_A-4263484 BB 0.003252 BB 559.044067 2309.156006
SNP_A-1978185 AA 0.004933 AA 1514.829102 250.839005
SNP_A-4264431 AA 0.014331 AA 2543.803955 335.166840
SNP_A-1980898 BB 0.004460 BB 219.581100 984.171204
SNP_A-1983139 AA 0.006148 AA 3817.153320 866.242798
SNP_A-4265735 AA 0.001550 AA 2700.263916 482.767914
SNP_A-1995832 BB 0.004085 BB 329.645294 1968.154175
SNP_A-1995893 BB 0.000607 BB 475.119202 3004.006348
SNP_A-1997689 BB 0.008864 BB 662.658081 4588.972656
SNP_A-1997709 AA 0.005440 AA 1655.416382 187.425919
SNP_A-1997896 AB 0.019809 AB 1496.025391 2119.912842
SNP_A-1997922 AB 0.015357 AB 983.317566 936.971130
SNP_A-2000230 AA 0.000356 AA 2758.854980 1074.415283
SNP_A-2000332 AB 0.027580 AB 2134.527588 2288.497803
SNP_A-2000337 AA 0.003538 AA 1588.223022 238.622833
SNP_A-2000342 AA 0.003031 AA 4082.553955 889.842224
SNP_A-4268173 AA 0.012101 AA 1930.365967 329.645294

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.

Supplementary file Size Download File type/resource
GSM397820.CEL.gz 30.3 Mb (ftp)(http) CEL
GSM397820.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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