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Sample GSM672417 Query DataSets for GSM672417
Status Public on Feb 17, 2011
Title 2894_Child_Father (Mapping250_Nsp)
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 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 AA 0.030048 AA 0.758919 11.858732
AFFX-2315061 AA 0.010458 AA 0.859870 11.056767
AFFX-2315062 AB 0.144300 AB -0.242179 10.333108
AFFX-2315057 BB 0.078093 BB -0.742486 10.716583
AFFX-2315058 AB 0.047828 AB 0.277777 11.251491
AFFX-2315059 AA 0.034272 AA 0.800270 10.601100
AFFX-2315063 AB 0.009225 AB -0.146751 10.746072
AFFX-2315064 AB 0.035016 AB 0.272656 11.045005
AFFX-2315065 BB 0.138820 BB -0.594050 10.143111
AFFX-2315066 BB 0.002507 BB -0.654354 10.440130
AFFX-2315067 AB 0.001214 AB 0.042896 11.018531
AFFX-2315068 AB 0.000417 AB 0.137183 10.586308
AFFX-2315069 BB 0.003081 BB -0.808911 10.608554
AFFX-2315070 BB 0.020330 BB -0.710524 10.542946
AFFX-2315071 AB 0.090394 AB -0.244866 9.474842
AFFX-2315072 AA 0.081005 AA 0.641015 10.536207
AFFX-2315073 AA 0.007124 AA 0.756119 10.595486
AFFX-2315074 BB 0.019175 BB -0.637747 10.202237
AFFX-2315075 BB 0.033394 BB -0.701550 11.324633
AFFX-2315076 BB 0.055650 BB -0.629287 10.562268

Total number of rows: 262314

Table truncated, full table size 12355 Kbytes.

Supplementary file Size Download File type/resource
GSM672417_2894_Father_Nsp.CEL.gz 24.9 Mb (ftp)(http) CEL
GSM672417_2894_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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