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Sample GSM672844 Query DataSets for GSM672844
Status Public on Feb 17, 2011
Title 1815_Father (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 1815
family member: Father
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 0.004323 BB -0.646321 12.229476
AFFX-2315061 AB 0.001240 AB 0.088320 11.298629
AFFX-2315062 AA 0.005013 AA 0.585250 10.782314
AFFX-2315057 AA 0.001169 AA 0.522964 10.818397
AFFX-2315058 AA 0.018316 AA 0.668409 11.446936
AFFX-2315059 AA 0.054467 AA 0.705765 10.662992
AFFX-2315063 AA 0.000394 AA 0.800812 10.809665
AFFX-2315064 AA 0.028722 AA 0.792919 11.277143
AFFX-2315065 AB 0.003001 AB -0.078847 10.574886
AFFX-2315066 BB 0.018119 BB -0.677783 10.862794
AFFX-2315067 BB 0.026873 BB -0.597220 11.258988
AFFX-2315068 AB 0.002608 AB 0.193201 10.937656
AFFX-2315069 AB 0.017140 AB -0.185113 10.966974
AFFX-2315070 AB 0.013580 AB -0.076876 11.041924
AFFX-2315071 AB 0.001604 AB -0.092794 9.966897
AFFX-2315072 AA 0.030957 AA 0.487298 11.055790
AFFX-2315073 BB 0.029090 BB -0.586045 11.027138
AFFX-2315074 AB 0.006358 AB 0.001569 10.657410
AFFX-2315075 AA 0.024016 AA 0.642153 11.825315
AFFX-2315076 AA 0.002380 AA 0.484978 10.933416

Total number of rows: 262314

Table truncated, full table size 12379 Kbytes.

Supplementary file Size Download File type/resource
GSM672844_1815_Father_Nsp.CEL.gz 27.0 Mb (ftp)(http) CEL
GSM672844_1815_Father_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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