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Sample GSM672467 Query DataSets for GSM672467
Status Public on Feb 17, 2011
Title 6932_Child (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 6932
family member: Child
gender: Female
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 0.006641 AB -0.075947 12.104568
AFFX-2315061 BB 0.003159 BB -0.845125 10.926997
AFFX-2315062 AA 0.012430 AA 0.653023 10.352755
AFFX-2315057 AB 0.005596 AB -0.063504 10.599310
AFFX-2315058 AA 0.002333 AA 0.785423 11.938138
AFFX-2315059 AB 0.002015 AB 0.237760 10.843570
AFFX-2315063 AB 0.006124 AB -0.216429 10.938854
AFFX-2315064 AB 0.002531 AB 0.259702 10.070544
AFFX-2315065 AB 0.037315 AB -0.145494 10.430614
AFFX-2315066 BB 0.040499 BB -0.783550 10.520933
AFFX-2315067 AB 0.028422 AB 0.071248 11.443846
AFFX-2315068 AA 0.006323 AA 0.855575 10.847898
AFFX-2315069 AA 0.053737 AA 0.574952 9.646255
AFFX-2315070 BB 0.005269 BB -0.623076 10.465560
AFFX-2315071 AA 0.006107 AA 0.818451 10.316619
AFFX-2315072 AA 0.000889 AA 0.746807 11.144773
AFFX-2315073 AB 0.001451 AB 0.126790 10.760585
AFFX-2315074 AB 0.008704 AB 0.049101 9.945487
AFFX-2315075 AB 0.006765 AB 0.130402 11.720641
AFFX-2315076 AA 0.006961 AA 0.639761 11.220451

Total number of rows: 238354

Table truncated, full table size 11217 Kbytes.

Supplementary file Size Download File type/resource
GSM672467_6932_Child_Sty.CEL.gz 25.8 Mb (ftp)(http) CEL
GSM672467_6932_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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