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Sample GSM672923 Query DataSets for GSM672923
Status Public on Feb 17, 2011
Title 9609_Child (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 9609
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 AB 0.000217 AB -0.112554 12.342103
AFFX-2315061 BB 0.002372 BB -0.765210 11.362590
AFFX-2315062 AB 0.097434 AB -0.158307 10.946991
AFFX-2315057 BB 0.162031 BB -0.532398 11.043694
AFFX-2315058 AA 0.014373 AA 0.723468 12.363780
AFFX-2315059 AB 0.020691 AB 0.236790 11.199306
AFFX-2315063 AA 0.056847 AA 0.789430 11.053639
AFFX-2315064 AB 0.176924 AB 0.358351 10.378721
AFFX-2315065 AB 0.012587 AB -0.054837 10.649428
AFFX-2315066 BB 0.034033 BB -0.623673 10.689998
AFFX-2315067 AB 0.044745 AB 0.030343 11.689588
AFFX-2315068 AA 0.018184 AA 0.840913 11.083511
AFFX-2315069 AB 0.019289 AB -0.182099 10.116618
AFFX-2315070 AB 0.066962 AB -0.107335 10.829229
AFFX-2315071 AB 0.033557 AB -0.190431 10.940239
AFFX-2315072 AA 0.208964 AA 0.764281 11.698386
AFFX-2315073 AB 0.045385 AB 0.096989 11.231219
AFFX-2315074 BB 0.015916 BB -0.490627 10.141437
AFFX-2315075 AA 0.111682 AA 0.689366 12.122396
AFFX-2315076 AA 0.075406 AA 0.604331 11.570541

Total number of rows: 238354

Table truncated, full table size 11248 Kbytes.

Supplementary file Size Download File type/resource
GSM672923_9609_Child_Sty.CEL.gz 25.6 Mb (ftp)(http) CEL
GSM672923_9609_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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