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Sample GSM672462 Query DataSets for GSM672462
Status Public on Feb 17, 2011
Title 2894_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2894
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 0.006048 AA 0.751396 11.946659
AFFX-2315061 AA 0.002295 AA 0.864564 11.044281
AFFX-2315062 AB 0.004214 AB -0.088063 10.469158
AFFX-2315057 BB 0.121010 BB -0.453287 10.576889
AFFX-2315058 AB 0.000665 AB 0.134526 11.890190
AFFX-2315059 AA 0.026805 AA 0.825812 10.653369
AFFX-2315063 AB 0.004467 AB -0.163415 10.719937
AFFX-2315064 AB 0.155017 AB 0.381642 10.053773
AFFX-2315065 BB 0.001834 BB -0.504014 10.319603
AFFX-2315066 BB 0.035013 BB -0.702047 10.212708
AFFX-2315067 AB 0.013010 AB 0.093024 11.324864
AFFX-2315068 AB 0.007824 AB 0.147854 10.480089
AFFX-2315069 BB 0.026986 BB -0.693223 9.701764
AFFX-2315070 BB 0.375897 BB -0.435422 10.492449
AFFX-2315071 AB 0.007365 AB -0.194012 10.102609
AFFX-2315072 AA 0.007085 AA 0.728010 11.095613
AFFX-2315073 AA 0.002495 AA 0.796724 10.555917
AFFX-2315074 BB 0.338042 BB -0.333736 9.904748
AFFX-2315075 BB 0.007954 BB -0.689327 11.548818
AFFX-2315076 BB 0.003187 BB -0.721664 11.181122

Total number of rows: 238354

Table truncated, full table size 11209 Kbytes.

Supplementary file Size Download File type/resource
GSM672462_2894_Father_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672462_2894_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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