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Sample GSM672470 Query DataSets for GSM672470
Status Public on Feb 17, 2011
Title 6942_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: 6942
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 0.025571 AA 0.625247 12.052559
AFFX-2315061 AA 0.000579 AA 0.873431 10.936552
AFFX-2315062 AA 0.001534 AA 0.661073 10.156308
AFFX-2315057 AB 0.014645 AB -0.056276 10.357515
AFFX-2315058 AB 0.003442 AB 0.132124 12.028562
AFFX-2315059 AB 0.020737 AB 0.085938 10.824186
AFFX-2315063 AA 0.002780 AA 0.771083 10.539304
AFFX-2315064 AB 0.113206 AB 0.316096 9.837310
AFFX-2315065 AB 0.028779 AB -0.137142 10.368587
AFFX-2315066 BB 0.016432 BB -0.736614 10.365289
AFFX-2315067 BB 0.001889 BB -0.626739 10.966945
AFFX-2315068 AA 0.000610 AA 0.856621 10.731872
AFFX-2315069 AB 0.358903 AB -0.359026 9.416939
AFFX-2315070 AB 0.041188 AB -0.143752 10.125868
AFFX-2315071 BB 0.005383 BB -0.857212 10.313823
AFFX-2315072 AB 0.014691 AB -0.044386 11.212509
AFFX-2315073 AB 0.014362 AB -0.008405 10.644698
AFFX-2315074 BB 0.056868 BB -0.448760 9.614061
AFFX-2315075 AA 0.007247 AA 0.692246 11.505710
AFFX-2315076 AB 0.023126 AB -0.103618 10.961515

Total number of rows: 238354

Table truncated, full table size 11211 Kbytes.

Supplementary file Size Download File type/resource
GSM672470_6942_Child_Sty.CEL.gz 26.0 Mb (ftp)(http) CEL
GSM672470_6942_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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