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Sample GSM672407 Query DataSets for GSM672407
Status Public on Feb 17, 2011
Title 2332_Child (Mapping250_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 2332
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 BB 0.071658 BB -0.682232 11.582938
AFFX-2315061 BB 0.018279 BB -0.747731 10.535889
AFFX-2315062 AB 0.004649 AB -0.062137 10.589644
AFFX-2315057 AB 0.096249 AB 0.029822 10.970152
AFFX-2315058 AA 0.036010 AA 0.706489 10.962056
AFFX-2315059 AB 0.016154 AB 0.223576 10.196656
AFFX-2315063 AA 0.000142 AA 0.769437 10.536662
AFFX-2315064 AB 0.014215 AB 0.245185 10.521152
AFFX-2315065 AB 0.001072 AB -0.063302 10.300834
AFFX-2315066 BB 0.026156 BB -0.633341 10.164715
AFFX-2315067 AB 0.015929 AB -0.009587 10.926171
AFFX-2315068 BB 0.024179 BB -0.742984 10.431435
AFFX-2315069 AA 0.030217 AA 0.657528 10.263426
AFFX-2315070 BB 0.098203 BB -0.542842 10.580486
AFFX-2315071 AB 0.001544 AB -0.133782 9.822186
AFFX-2315072 AB 0.010107 AB -0.026129 10.873743
AFFX-2315073 AA 0.021919 AA 0.736889 10.414869
AFFX-2315074 AB 0.006414 AB 0.099618 10.224489
AFFX-2315075 AA 0.035620 AA 0.724876 11.593691
AFFX-2315076 AB 0.204322 AB -0.146082 10.631885

Total number of rows: 262314

Table truncated, full table size 12346 Kbytes.

Supplementary file Size Download File type/resource
GSM672407_2332_Child_Nsp.CEL.gz 24.3 Mb (ftp)(http) CEL
GSM672407_2332_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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