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Sample GSM672461 Query DataSets for GSM672461
Status Public on Feb 17, 2011
Title 2894_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: 2894
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 AA 0.027003 AA 0.796616 11.745299
AFFX-2315061 AB 0.034859 AB 0.277008 10.848024
AFFX-2315062 BB 0.004035 BB -0.661389 10.204735
AFFX-2315057 AB 0.010975 AB -0.119981 10.582937
AFFX-2315058 AA 0.034983 AA 0.826261 11.827687
AFFX-2315059 AB 0.016132 AB 0.308054 10.634907
AFFX-2315063 AB 0.003893 AB -0.115503 10.762133
AFFX-2315064 AB 0.076003 AB 0.196052 9.886982
AFFX-2315065 AB 0.021437 AB -0.020224 10.243477
AFFX-2315066 BB 0.006083 BB -0.687989 10.325458
AFFX-2315067 BB 0.015219 BB -0.669761 10.941566
AFFX-2315068 AA 0.000950 AA 0.854073 10.673392
AFFX-2315069 BB 0.046666 BB -0.687539 9.597193
AFFX-2315070 BB 0.099444 BB -0.511933 10.526443
AFFX-2315071 AB 0.007095 AB -0.165400 10.083581
AFFX-2315072 AA 0.012660 AA 0.786019 11.090400
AFFX-2315073 AB 0.009104 AB 0.106385 10.426468
AFFX-2315074 BB 0.005188 BB -0.468193 9.793442
AFFX-2315075 AB 0.001044 AB 0.098416 11.611241
AFFX-2315076 BB 0.000916 BB -0.692608 11.042253

Total number of rows: 238354

Table truncated, full table size 11207 Kbytes.

Supplementary file Size Download File type/resource
GSM672461_2894_Child_Sty.CEL.gz 24.9 Mb (ftp)(http) CEL
GSM672461_2894_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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