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Sample GSM672409 Query DataSets for GSM672409
Status Public on Feb 17, 2011
Title 2332_Child_Mother (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2332
family member: Mother
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 0.002554 AB -0.035210 11.838157
AFFX-2315061 BB 0.007770 BB -0.796167 10.932100
AFFX-2315062 AB 0.027718 AB -0.180500 10.580373
AFFX-2315057 BB 0.037291 BB -0.671008 10.994421
AFFX-2315058 AA 0.003297 AA 0.698813 11.275217
AFFX-2315059 AA 0.009550 AA 0.770927 10.420218
AFFX-2315063 AA 0.004933 AA 0.781422 10.644743
AFFX-2315064 AA 0.005060 AA 0.819563 10.792390
AFFX-2315065 AA 0.050430 AA 0.631210 10.278682
AFFX-2315066 BB 0.002483 BB -0.666893 10.369573
AFFX-2315067 AA 0.009017 AA 0.520428 10.933837
AFFX-2315068 AB 0.035898 AB -0.013311 10.618276
AFFX-2315069 AB 0.005327 AB -0.188784 10.520044
AFFX-2315070 AB 0.001867 AB -0.098617 10.638337
AFFX-2315071 BB 0.019198 BB -0.713347 9.946620
AFFX-2315072 AB 0.046732 AB 0.084613 10.724775
AFFX-2315073 AA 0.003339 AA 0.728654 10.504006
AFFX-2315074 AB 0.001715 AB 0.029903 10.356691
AFFX-2315075 AA 0.048466 AA 0.642226 11.693889
AFFX-2315076 BB 0.017331 BB -0.555313 10.555135

Total number of rows: 262314

Table truncated, full table size 12368 Kbytes.

Supplementary file Size Download File type/resource
GSM672409_2332_Mother_Nsp.CEL.gz 25.8 Mb (ftp)(http) CEL
GSM672409_2332_Mother_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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