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Sample GSM672413 Query DataSets for GSM672413
Status Public on Feb 17, 2011
Title 2569_Child (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 2569
family member: Child
gender: Male
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 0.033934 AB -0.193638 12.132171
AFFX-2315061 BB 0.000895 BB -0.792970 11.175442
AFFX-2315062 BB 0.006851 BB -0.591775 10.800667
AFFX-2315057 BB 0.012551 BB -0.664420 11.104782
AFFX-2315058 AA 0.023118 AA 0.662907 11.437291
AFFX-2315059 AB 0.010865 AB 0.319833 10.549387
AFFX-2315063 AA 0.012674 AA 0.755263 10.896491
AFFX-2315064 AB 0.149840 AB 0.424112 11.007740
AFFX-2315065 AB 0.033421 AB 0.026108 10.648646
AFFX-2315066 AB 0.029424 AB 0.104520 10.563755
AFFX-2315067 AB 0.010149 AB 0.091459 11.265200
AFFX-2315068 AB 0.006738 AB 0.214592 10.766688
AFFX-2315069 AB 0.007661 AB -0.078546 10.598713
AFFX-2315070 BB 0.018610 BB -0.621139 10.838738
AFFX-2315071 AB 0.003641 AB -0.158168 9.985415
AFFX-2315072 AB 0.026658 AB -0.123795 11.092498
AFFX-2315073 AA 0.035237 AA 0.730761 10.696398
AFFX-2315074 BB 0.023253 BB -0.554162 10.582220
AFFX-2315075 AA 0.152712 AA 0.628353 12.047109
AFFX-2315076 AB 0.054510 AB 0.133880 10.954694

Total number of rows: 262314

Table truncated, full table size 12370 Kbytes.

Supplementary file Size Download File type/resource
GSM672413_2569_Child_Nsp.CEL.gz 25.1 Mb (ftp)(http) CEL
GSM672413_2569_Child_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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