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Sample GSM672857 Query DataSets for GSM672857
Status Public on Feb 17, 2011
Title 5993_Child (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 5993
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 0.011763 AB -0.099065 12.281739
AFFX-2315061 BB 0.001586 BB -0.767883 11.088323
AFFX-2315062 BB 0.014476 BB -0.646534 10.657687
AFFX-2315057 AB 0.017070 AB -0.203961 10.882646
AFFX-2315058 AA 0.014797 AA 0.731657 11.593558
AFFX-2315059 AB 0.001258 AB 0.265328 10.586004
AFFX-2315063 AA 0.021875 AA 0.763788 10.576756
AFFX-2315064 AB 0.018175 AB 0.165038 10.888238
AFFX-2315065 AB 0.050709 AB -0.130522 10.507559
AFFX-2315066 BB 0.033839 BB -0.627087 10.462047
AFFX-2315067 AB 0.044786 AB 0.041542 11.035107
AFFX-2315068 BB 0.001154 BB -0.637200 10.799949
AFFX-2315069 AB 0.001032 AB -0.119272 10.692410
AFFX-2315070 AB 0.033855 AB -0.112997 10.680845
AFFX-2315071 BB 0.003474 BB -0.740964 9.932590
AFFX-2315072 AA 0.030258 AA 0.467744 10.902580
AFFX-2315073 AA 0.015282 AA 0.710444 10.800433
AFFX-2315074 BB 0.055766 BB -0.643743 10.398966
AFFX-2315075 AB 0.018209 AB 0.005189 11.815447
AFFX-2315076 AA 0.057532 AA 0.429744 10.793116

Total number of rows: 262314

Table truncated, full table size 12379 Kbytes.

Supplementary file Size Download File type/resource
GSM672857_5993_Child_Nsp.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM672857_5993_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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