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Sample GSM672476 Query DataSets for GSM672476
Status Public on Feb 17, 2011
Title 8160_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: 8160
family member: Child
gender: unknown
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 0.004219 AA 0.690553 11.775146
AFFX-2315061 AA 0.004301 AA 0.881051 11.101541
AFFX-2315062 AA 0.030643 AA 0.570327 10.254898
AFFX-2315057 AB 0.015495 AB -0.002594 10.469360
AFFX-2315058 AA 0.008262 AA 0.801625 11.921086
AFFX-2315059 AB 0.007344 AB 0.286591 10.798630
AFFX-2315063 AB 0.003211 AB -0.111197 10.804745
AFFX-2315064 AA 0.034693 AA 0.768932 10.255392
AFFX-2315065 AB 0.095258 AB -0.129845 10.163395
AFFX-2315066 BB 0.035644 BB -0.723630 10.246431
AFFX-2315067 BB 0.006497 BB -0.624322 10.909045
AFFX-2315068 AB 0.001495 AB 0.144651 10.623217
AFFX-2315069 AA 0.014032 AA 0.640152 9.609121
AFFX-2315070 BB 0.000780 BB -0.603143 10.426510
AFFX-2315071 AB 0.006986 AB -0.241113 10.287563
AFFX-2315072 AA 0.006971 AA 0.752053 11.044711
AFFX-2315073 AA 0.011359 AA 0.777503 10.425813
AFFX-2315074 AB 0.012917 AB 0.130475 9.948624
AFFX-2315075 AB 0.003285 AB 0.113696 11.679475
AFFX-2315076 AB 0.011170 AB -0.047170 10.987091

Total number of rows: 238354

Table truncated, full table size 11208 Kbytes.

Supplementary file Size Download File type/resource
GSM672476_8160_Child_Sty.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM672476_8160_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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