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Sample GSM397823 Query DataSets for GSM397823
Status Public on Jul 31, 2010
Title Blood-Ctrl-1840-rep1
Sample type genomic
 
Source name Ctrl Blood
Organism Homo sapiens
Characteristics study #: Study 3 (Trio)
trio #: Trio 7 / Father
twin #: NA
twin info: NA
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
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 BB 0.002718 BB 573.801025 4071.961914
SNP_A-1967418 AB 0.002252 AB 510.666016 478.116791
SNP_A-1969580 BB 0.004931 BB 918.282410 3976.661133
SNP_A-4263484 AB 0.000853 AB 1830.550659 1365.383545
SNP_A-1978185 AA 0.004091 AA 1607.278564 315.714691
SNP_A-4264431 AA 0.002770 AA 2011.346558 363.396393
SNP_A-1980898 AB 0.001788 AB 677.414124 573.801880
SNP_A-1983139 AA 0.003394 AA 4766.836426 995.696716
SNP_A-4265735 AB 0.005237 AB 2017.174927 1824.581543
SNP_A-1995832 AA 0.011112 AA 2169.388672 374.967041
SNP_A-1995893 AA 0.005502 AA 2838.233887 1166.312988
SNP_A-1997689 BB 0.006427 BB 533.049316 3562.746338
SNP_A-1997709 AA 0.003909 AA 2520.169434 268.265930
SNP_A-1997896 AA 0.003341 AA 1203.009399 350.215302
SNP_A-1997922 AA 0.000678 AA 1047.180420 265.085266
SNP_A-2000230 AA 0.004926 AA 3139.645020 1055.207397
SNP_A-2000332 AB 0.006398 AB 3168.594971 3468.560059
SNP_A-2000337 AA 0.000726 AA 1819.164185 263.494659
SNP_A-2000342 AA 0.004055 AA 4486.879395 958.553772
SNP_A-4268173 AA 0.003864 AA 1476.864258 204.179413

Total number of rows: 909622

Table truncated, full table size 46130 Kbytes.




Supplementary file Size Download File type/resource
GSM397823.CEL.gz 28.7 Mb (ftp)(http) CEL
GSM397823.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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