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Sample GSM397688 Query DataSets for GSM397688
Status Public on Jul 31, 2010
Title Brain-MND-0794-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: 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 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 0.003468 BB 524.225952 4028.124023
SNP_A-1967418 BB 0.000453 BB 260.285248 718.937256
SNP_A-1969580 BB 0.006320 BB 1350.143677 3968.251953
SNP_A-4263484 BB 0.011082 BB 529.850952 1760.067017
SNP_A-1978185 AA 0.002781 AA 1064.621704 337.685028
SNP_A-4264431 AB 0.010455 AB 851.319946 723.563843
SNP_A-1980898 AB 0.006585 AB 447.980804 369.181244
SNP_A-1983139 AA 0.004380 AA 5400.374023 1376.831787
SNP_A-4265735 BB 0.003807 BB 653.173462 3146.366699
SNP_A-1995832 AB 0.000852 AB 1989.229370 1505.674438
SNP_A-1995893 AB 0.001330 AB 1852.933472 2067.995117
SNP_A-1997689 BB 0.001078 BB 735.049500 4102.647949
SNP_A-1997709 AA 0.003115 AA 2812.833740 327.129761
SNP_A-1997896 AA 0.002602 AA 1253.532593 544.700562
SNP_A-1997922 AB 0.002481 AB 707.675415 533.257141
SNP_A-2000230 AA 0.010765 AA 2101.720703 796.434692
SNP_A-2000332 AB 0.000563 AB 2935.885254 3019.799561
SNP_A-2000337 AA 0.006311 AA 1967.700562 205.773239
SNP_A-2000342 AA 0.015697 AA 3869.427490 1342.223389
SNP_A-4268173 AA 0.003892 AA 1061.723877 185.828384

Total number of rows: 909622

Table truncated, full table size 46128 Kbytes.

Supplementary file Size Download File type/resource
GSM397688.CEL.gz 29.8 Mb (ftp)(http) CEL
GSM397688.CHP.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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