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Sample GSM397786 Query DataSets for GSM397786
Status Public on Jul 31, 2010
Title Blood-Ctrl-1467-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 3
twin info: Monozygotic Control
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 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 0.003456 AB 2456.106445 2616.979736
SNP_A-1967418 BB 0.000763 BB 275.555481 742.428345
SNP_A-1969580 BB 0.003601 BB 938.650269 3651.253418
SNP_A-4263484 AB 0.003602 AB 1567.178345 1115.995239
SNP_A-1978185 AA 0.003072 AA 1296.921387 422.466675
SNP_A-4264431 AB 0.001356 AB 1238.862305 887.257507
SNP_A-1980898 AB 0.001126 AB 603.068604 483.164276
SNP_A-1983139 AA 0.004138 AA 4201.442383 1174.683105
SNP_A-4265735 AA 0.004195 AA 2515.740723 577.577942
SNP_A-1995832 AB 0.000644 AB 1898.668457 1404.104614
SNP_A-1995893 AB 0.000865 AB 2068.776123 2263.226074
SNP_A-1997689 BB 0.001135 BB 766.866577 4102.647949
SNP_A-1997709 AA 0.001675 AA 2718.212158 347.331116
SNP_A-1997896 AA 0.003867 AA 1167.259888 338.927307
SNP_A-1997922 AB 0.002561 AB 668.170959 523.510376
SNP_A-2000230 AA 0.001229 AA 2576.452881 1032.803589
SNP_A-2000332 AA 0.005200 AA 4354.854980 825.938171
SNP_A-2000337 AA 0.002542 AA 1676.326660 238.737701
SNP_A-2000342 AA 0.004098 AA 4514.324707 972.009888
SNP_A-4268173 AB 0.001284 AB 880.832153 778.580688

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.

Supplementary file Size Download File type/resource
GSM397786.CEL.gz 31.2 Mb (ftp)(http) CEL
GSM397786.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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