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Sample GSM672411 Query DataSets for GSM672411
Status Public on Feb 17, 2011
Title 2377_Child_Father (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2377
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 0.004034 AB -0.028776 11.910451
AFFX-2315061 BB 0.009199 BB -0.824115 10.925518
AFFX-2315062 AB 0.068561 AB 0.063707 10.581904
AFFX-2315057 AA 0.009864 AA 0.592390 10.568746
AFFX-2315058 AA 0.019818 AA 0.657173 11.246511
AFFX-2315059 AA 0.001835 AA 0.745533 10.447079
AFFX-2315063 AA 0.019900 AA 0.813987 10.766833
AFFX-2315064 AB 0.013835 AB 0.216051 10.957616
AFFX-2315065 AB 0.076421 AB -0.151153 10.362679
AFFX-2315066 BB 0.022561 BB -0.724672 10.455749
AFFX-2315067 AB 0.066587 AB -0.083102 11.132873
AFFX-2315068 AB 0.000467 AB 0.166061 10.589047
AFFX-2315069 AB 0.008814 AB -0.048261 10.658784
AFFX-2315070 BB 0.031880 BB -0.728692 10.736832
AFFX-2315071 BB 0.017699 BB -0.766076 9.962186
AFFX-2315072 AB 0.013636 AB -0.084534 10.625629
AFFX-2315073 AA 0.028634 AA 0.768589 10.713541
AFFX-2315074 BB 0.021429 BB -0.662756 10.311221
AFFX-2315075 AA 0.014350 AA 0.672674 11.620031
AFFX-2315076 BB 0.029422 BB -0.595951 10.635110

Total number of rows: 262314

Table truncated, full table size 12367 Kbytes.

Supplementary file Size Download File type/resource
GSM672411_2377_Father_Nsp.CEL.gz 26.1 Mb (ftp)(http) CEL
GSM672411_2377_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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