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Sample GSM397794 Query DataSets for GSM397794
Status Public on Jul 31, 2010
Title Hair-Ctrl-1901-rep1
Sample type genomic
Source name Ctrl Hair
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 4
twin info: Monozygotic Discordant for MND
gender: M
phenotype: Ctrl
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 Ctrl Hair
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 0.002476 AB 2870.505859 2766.990234
SNP_A-1967418 AB 0.065792 AB 619.870422 389.958252
SNP_A-1969580 BB 0.001138 BB 1186.056519 4251.510254
SNP_A-4263484 AB 0.002036 AB 2109.443604 1539.647461
SNP_A-1978185 AB 0.005651 AB 942.273376 1394.875000
SNP_A-4264431 AB 0.001726 AB 1102.319336 885.130920
SNP_A-1980898 AB 0.004429 AB 566.793945 396.314301
SNP_A-1983139 AB 0.005944 AB 3184.858154 3059.280518
SNP_A-4265735 AA 0.004695 AA 3256.673340 762.393738
SNP_A-1995832 BB 0.003993 BB 773.520386 2620.024658
SNP_A-1995893 BB 0.008769 BB 615.967224 3614.093750
SNP_A-1997689 BB 0.005074 BB 653.397339 3414.304688
SNP_A-1997709 AA 0.004213 AA 1719.656494 281.643250
SNP_A-1997896 AA 0.001344 AA 1221.790039 444.493225
SNP_A-1997922 BB 0.006454 BB 487.901398 966.816406
SNP_A-2000230 AA 0.003863 AA 2418.239990 909.152344
SNP_A-2000332 AB 0.005688 AB 2978.440918 3455.377441
SNP_A-2000337 AA 0.006241 AA 1588.911255 203.502747
SNP_A-2000342 AA 0.003335 AA 4258.368652 901.230408
SNP_A-4268173 AA 0.009840 AA 942.273376 240.107162

Total number of rows: 909622

Table truncated, full table size 46118 Kbytes.

Supplementary file Size Download File type/resource
GSM397794.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM397794.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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