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Sample GSM397785 Query DataSets for GSM397785
Status Public on Jul 31, 2010
Title Blood-Ctrl-1418-rep1
Sample type genomic
 
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 2 (Twin)
trio #: NA
twin #: Twin 2
twin info: Dizygotic Discordant for MND
gender: F
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
ID_REF PROBE SET NAME
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
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AB 0.004343 AB 3254.916504 3520.782227
SNP_A-1967418 BB 0.015765 BB 369.703125 986.316101
SNP_A-1969580 BB 0.001720 BB 1240.479126 4309.441895
SNP_A-4263484 BB 0.005379 BB 587.368408 2407.762695
SNP_A-1978185 AA 0.007835 AA 1801.730835 477.503845
SNP_A-4264431 AB 0.000353 AB 1221.007690 924.554138
SNP_A-1980898 AB 0.003329 AB 587.332214 606.021057
SNP_A-1983139 AA 0.006800 AA 4570.861328 1460.407593
SNP_A-4265735 AB 0.006853 AB 2298.583252 2432.546143
SNP_A-1995832 AB 0.010167 AB 2412.344482 2039.296631
SNP_A-1995893 AB 0.011364 AB 2477.791504 2861.561035
SNP_A-1997689 BB 0.018696 BB 893.356934 5082.988770
SNP_A-1997709 AA 0.009803 AA 3027.058838 285.948639
SNP_A-1997896 AA 0.007098 AA 1362.863403 676.684937
SNP_A-1997922 AB 0.016515 AB 828.736938 918.896240
SNP_A-2000230 AA 0.012737 AA 3430.018555 1318.324341
SNP_A-2000332 AA 0.061076 AA 4421.597168 1648.932129
SNP_A-2000337 AA 0.010153 AA 1840.690796 386.889832
SNP_A-2000342 AA 0.011527 AA 4652.568848 1388.655151
SNP_A-4268173 AA 0.002014 AA 1336.989380 283.923157

Total number of rows: 909622

Table truncated, full table size 46130 Kbytes.




Supplementary file Size Download File type/resource
GSM397785.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM397785.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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