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Sample GSM672465 Query DataSets for GSM672465
Status Public on Feb 17, 2011
Title 4821_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 4821
family member: Father
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label Biotin
Label protocol DNA samples were processed according to the instructions provided in the Affymetrix GeneChip® Mapping 500K Assay Manual
Hybridization protocol hybridized to GeneChip® Human Mapping 250K Nsp or 250K Sty arrays in an Affymetrix Hybridization Oven 640
Scan protocol images were obtained using an Affymetrix GeneChip® Scanner 3000 7G and GeneChip® Operating Software version 1.4
Data processing CNVs were detected using the Copy Number Analysis Tool (CNAT) (release cn-1.5.6_v3.2), which incorporates a Bayesian Robust Linear Model with the Mahalanobis distance classifier (BRLMM) algorithm to perform quantile normalization, followed by regression to reduce the PCR bias due to GC content and fragment length
An HMM-based algorithm implemented in CNAT4 was used to estimate copy number for each SNP in the context of its surrounding SNPs. The Gaussian bandwidth was set to 0 Kb and a minimum of 5 probes was required to detect a CNV. The findings were visualized using GeneChip Genotyping Analysis Software (GTYPE) from Affymetrix.
Submission date Feb 10, 2011
Last update date Feb 17, 2011
Contact name Tracy Tucker
Organization name University of British Columbia
Street address Box 153 4480 Oak Street
City Vancouver
ZIP/Postal code V6H3V4
Country Canada
Platform ID GPL3720
Series (2)
GSE27216 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Mapping250K_Nsp and Mapping250K_Sty)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions

Data table
AFFX-2315060 AA 0.013043 AA 0.565079 12.360126
AFFX-2315061 AB 0.003401 AB 0.102516 11.844157
AFFX-2315062 AA 0.004961 AA 0.579039 10.403514
AFFX-2315057 BB 0.007695 BB -0.453665 10.561647
AFFX-2315058 AA 0.060470 AA 0.701081 12.526572
AFFX-2315059 BB 0.011184 BB -0.667542 10.992508
AFFX-2315063 AA 0.016504 AA 0.813895 10.699582
AFFX-2315064 BB 0.002635 BB -0.356810 10.053087
AFFX-2315065 AB 0.046861 AB 0.024283 10.744102
AFFX-2315066 BB 0.012291 BB -0.672908 10.525660
AFFX-2315067 AB 0.000363 AB 0.022326 11.378355
AFFX-2315068 BB 0.011398 BB -0.766041 10.948430
AFFX-2315069 AB 0.010725 AB -0.097520 10.654474
AFFX-2315070 AB 0.050555 AB -0.171111 10.626538
AFFX-2315071 AB 0.007066 AB -0.245842 10.481147
AFFX-2315072 AA 0.006974 AA 0.609755 10.865714
AFFX-2315073 AA 0.000427 AA 0.710856 10.568276
AFFX-2315074 AB 0.080718 AB 0.222109 9.953178
AFFX-2315075 AB 0.002373 AB 0.048334 11.485056
AFFX-2315076 AA 0.028675 AA 0.645698 11.104801

Total number of rows: 238354

Table truncated, full table size 11258 Kbytes.

Supplementary file Size Download File type/resource
GSM672465_4821_Father_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672465_4821_Father_Sty.chp.gz 3.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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