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Sample GSM397824 Query DataSets for GSM397824
Status Public on Jul 31, 2010
Title Blood-Ctrl-1841-rep1
Sample type genomic
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 7 / Mother
twin #: NA
twin info: NA
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
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 0.004488 BB 831.745239 4507.758789
SNP_A-1967418 BB 0.004614 BB 243.373566 837.195007
SNP_A-1969580 BB 0.008646 BB 957.808838 3173.296631
SNP_A-4263484 AB 0.005224 AB 1541.483887 1034.898926
SNP_A-1978185 AA 0.003376 AA 1589.031616 411.410187
SNP_A-4264431 AA 0.002851 AA 2042.236450 358.614685
SNP_A-1980898 AB 0.012600 AB 829.223877 764.617920
SNP_A-1983139 AA 0.002653 AA 4238.453613 1081.509033
SNP_A-4265735 AA 0.006142 AA 2278.069336 453.185791
SNP_A-1995832 AB 0.002990 AB 1589.031616 1221.627563
SNP_A-1995893 AB 0.003898 AB 1664.717163 1910.118652
SNP_A-1997689 BB 0.011230 BB 1013.233459 4442.243652
SNP_A-1997709 AA 0.002756 AA 2476.405273 277.837555
SNP_A-1997896 AB 0.004867 AB 1186.847656 1514.180542
SNP_A-1997922 AA 0.006931 AA 888.543884 284.086609
SNP_A-2000230 AA 0.002059 AA 2680.923340 1151.790894
SNP_A-2000332 AA 0.001954 AA 4273.625000 1015.635681
SNP_A-2000337 AA 0.005081 AA 1998.492554 334.564911
SNP_A-2000342 AA 0.005320 AA 4567.866211 955.028320
SNP_A-4268173 AA 0.024830 AA 2148.988281 334.176880

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.

Supplementary file Size Download File type/resource
GSM397824.CEL.gz 31.7 Mb (ftp)(http) CEL
GSM397824.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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