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Sample GSM672837 Query DataSets for GSM672837
Status Public on Feb 17, 2011
Title 1056_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: 1056
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 0.009228 AB -0.008376 12.215817
AFFX-2315061 AB 0.006598 AB 0.164240 11.342122
AFFX-2315062 AA 0.010434 AA 0.607536 10.819308
AFFX-2315057 AB 0.028262 AB -0.114333 11.112316
AFFX-2315058 AA 0.025956 AA 0.726205 11.472412
AFFX-2315059 AA 0.013724 AA 0.782825 10.664156
AFFX-2315063 AA 0.006760 AA 0.793990 10.922810
AFFX-2315064 AA 0.014908 AA 0.772813 11.166419
AFFX-2315065 AA 0.000700 AA 0.460821 10.504635
AFFX-2315066 AB 0.004155 AB -0.018287 10.798400
AFFX-2315067 AB 0.012730 AB -0.022711 11.161564
AFFX-2315068 AB 0.005161 AB 0.120307 10.925291
AFFX-2315069 AA 0.008539 AA 0.793821 10.757594
AFFX-2315070 AB 0.013315 AB -0.091460 11.045438
AFFX-2315071 AB 0.002106 AB -0.155306 9.943994
AFFX-2315072 AA 0.000982 AA 0.532093 10.972992
AFFX-2315073 AA 0.001038 AA 0.748437 10.880772
AFFX-2315074 BB 0.004477 BB -0.606354 10.615173
AFFX-2315075 AA 0.025368 AA 0.738659 11.749588
AFFX-2315076 AA 0.033418 AA 0.497891 11.124290

Total number of rows: 262314

Table truncated, full table size 12381 Kbytes.

Supplementary file Size Download File type/resource
GSM672837_1056_Child_Nsp.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672837_1056_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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