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Sample GSM672841 Query DataSets for GSM672841
Status Public on Feb 17, 2011
Title 1780_Father (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 1780
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 GPL3718
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 AB 0.003162 AB -0.119805 12.135369
AFFX-2315061 AB 0.007917 AB 0.141202 11.125186
AFFX-2315062 AA 0.003591 AA 0.559739 10.748741
AFFX-2315057 AB 0.034373 AB -0.033135 10.892653
AFFX-2315058 AB 0.002733 AB 0.132134 11.318913
AFFX-2315059 AA 0.110785 AA 0.737848 10.414240
AFFX-2315063 AB 0.023618 AB 0.121715 10.887426
AFFX-2315064 AB 0.015804 AB 0.149837 10.931793
AFFX-2315065 AB 0.008473 AB -0.089703 10.548149
AFFX-2315066 BB 0.000026 BB -0.661174 10.677127
AFFX-2315067 AB 0.021450 AB 0.115624 11.222187
AFFX-2315068 AA 0.019389 AA 0.811361 10.685125
AFFX-2315069 AB 0.003837 AB -0.142961 10.625205
AFFX-2315070 AB 0.004377 AB -0.094459 10.828795
AFFX-2315071 AA 0.024013 AA 0.689037 9.579522
AFFX-2315072 AB 0.001970 AB -0.087571 10.992245
AFFX-2315073 AA 0.004100 AA 0.756574 10.853685
AFFX-2315074 AA 0.016451 AA 0.730640 10.479565
AFFX-2315075 AA 0.109408 AA 0.609638 11.918688
AFFX-2315076 AB 0.035870 AB 0.091926 11.090104

Total number of rows: 262314

Table truncated, full table size 12375 Kbytes.

Supplementary file Size Download File type/resource
GSM672841_1780_Father_Nsp.CEL.gz 25.8 Mb (ftp)(http) CEL
GSM672841_1780_Father_Nsp.chp.gz 4.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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