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Sample GSM672893 Query DataSets for GSM672893
Status Public on Feb 17, 2011
Title 3094_Child (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 3094
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 GPL3720
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 0.009005 AB -0.040562 12.334572
AFFX-2315061 AB 0.003493 AB 0.163980 11.828631
AFFX-2315062 AB 0.001263 AB -0.041105 10.492253
AFFX-2315057 BB 0.087129 BB -0.358821 10.443106
AFFX-2315058 AB 0.001381 AB 0.169076 12.228770
AFFX-2315059 AA 0.004902 AA 0.779374 11.045390
AFFX-2315063 AA 0.009664 AA 0.797337 10.800730
AFFX-2315064 AB 0.193777 AB 0.361778 10.310308
AFFX-2315065 AB 0.007437 AB 0.015061 10.598534
AFFX-2315066 BB 0.063753 BB -0.744647 10.620663
AFFX-2315067 BB 0.008738 BB -0.602317 11.270473
AFFX-2315068 AB 0.003359 AB 0.079097 10.895144
AFFX-2315069 AB 0.008177 AB -0.165560 10.203279
AFFX-2315070 BB 0.017252 BB -0.583516 10.604999
AFFX-2315071 AB 0.006036 AB -0.175657 10.608905
AFFX-2315072 AB 0.013915 AB 0.106872 11.220888
AFFX-2315073 AB 0.002877 AB 0.109185 10.686261
AFFX-2315074 BB 0.026866 BB -0.496845 9.989643
AFFX-2315075 AB 0.051693 AB -0.050674 11.856812
AFFX-2315076 AA 0.003868 AA 0.568523 11.186881

Total number of rows: 238354

Table truncated, full table size 11262 Kbytes.

Supplementary file Size Download File type/resource
GSM672893_3094_Child_Sty.CEL.gz 27.0 Mb (ftp)(http) CEL
GSM672893_3094_Child_Sty.chp.gz 3.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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