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Sample GSM672843 Query DataSets for GSM672843
Status Public on Feb 17, 2011
Title 1815_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: 1815
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 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 0.027510 AB -0.179759 12.215816
AFFX-2315061 AA 0.001997 AA 0.831799 11.261792
AFFX-2315062 AB 0.004950 AB -0.019174 10.836437
AFFX-2315057 AA 0.002221 AA 0.496793 10.776133
AFFX-2315058 AA 0.076679 AA 0.736538 11.348802
AFFX-2315059 AB 0.010507 AB 0.260086 10.469503
AFFX-2315063 AB 0.015840 AB -0.070149 10.843842
AFFX-2315064 AB 0.001912 AB 0.221606 10.993915
AFFX-2315065 AA 0.084017 AA 0.367309 10.570336
AFFX-2315066 BB 0.007059 BB -0.654699 10.786943
AFFX-2315067 AB 0.099681 AB 0.174387 11.307336
AFFX-2315068 AB 0.021392 AB 0.282741 10.825274
AFFX-2315069 AA 0.001734 AA 0.779050 10.669101
AFFX-2315070 AA 0.009647 AA 0.664523 10.890464
AFFX-2315071 AB 0.003161 AB -0.145725 9.806725
AFFX-2315072 AA 0.008446 AA 0.499242 10.996799
AFFX-2315073 BB 0.006044 BB -0.635527 10.740959
AFFX-2315074 AA 0.002221 AA 0.724325 10.277333
AFFX-2315075 AB 0.003282 AB 0.064613 11.771206
AFFX-2315076 AB 0.027897 AB 0.108138 10.997297

Total number of rows: 262314

Table truncated, full table size 12373 Kbytes.

Supplementary file Size Download File type/resource
GSM672843_1815_Child_Nsp.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM672843_1815_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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