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Sample GSM672452 Query DataSets for GSM672452
Status Public on Feb 17, 2011
Title 2332_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: 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 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 BB 0.005679 BB -0.737552 11.976065
AFFX-2315061 BB 0.001906 BB -0.794177 10.751118
AFFX-2315062 AB 0.003784 AB -0.087381 10.251325
AFFX-2315057 AB 0.045459 AB -0.103243 10.270410
AFFX-2315058 AA 0.003089 AA 0.755612 12.001986
AFFX-2315059 AB 0.003213 AB 0.269696 10.709430
AFFX-2315063 AA 0.000847 AA 0.821850 10.549726
AFFX-2315064 AB 0.022683 AB 0.312403 9.991517
AFFX-2315065 AB 0.039455 AB -0.018004 10.182439
AFFX-2315066 BB 0.006387 BB -0.680932 10.436907
AFFX-2315067 AB 0.000349 AB 0.038500 11.195752
AFFX-2315068 BB 0.004387 BB -0.788719 10.405214
AFFX-2315069 AA 0.028431 AA 0.655352 9.494538
AFFX-2315070 BB 0.044929 BB -0.578511 10.193312
AFFX-2315071 AB 0.000213 AB -0.160526 10.348624
AFFX-2315072 AB 0.001048 AB 0.055581 11.096109
AFFX-2315073 AA 0.000914 AA 0.795903 10.596805
AFFX-2315074 AB 0.027308 AB 0.032492 9.643460
AFFX-2315075 AA 0.000495 AA 0.731929 11.470897
AFFX-2315076 AB 0.020798 AB -0.106940 10.996662

Total number of rows: 238354

Table truncated, full table size 11208 Kbytes.

Supplementary file Size Download File type/resource
GSM672452_2332_Child_Sty.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM672452_2332_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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