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Sample GSM672468 Query DataSets for GSM672468
Status Public on Feb 17, 2011
Title 6932_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 6932
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 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 0.006716 AA 0.751665 11.978235
AFFX-2315061 BB 0.000419 BB -0.800908 10.881550
AFFX-2315062 AB 0.061522 AB 0.104177 10.416101
AFFX-2315057 AB 0.003408 AB -0.058657 10.567837
AFFX-2315058 AA 0.000393 AA 0.772760 11.986952
AFFX-2315059 AB 0.013644 AB 0.302523 10.826118
AFFX-2315063 AA 0.012272 AA 0.821944 10.791913
AFFX-2315064 AA 0.013316 AA 0.749957 10.106460
AFFX-2315065 BB 0.011699 BB -0.502774 10.475639
AFFX-2315066 BB 0.055490 BB -0.670778 10.590765
AFFX-2315067 AA 0.002327 AA 0.622577 11.272155
AFFX-2315068 AA 0.000190 AA 0.845074 10.725694
AFFX-2315069 AB 0.045558 AB 0.060002 9.615741
AFFX-2315070 BB 0.009542 BB -0.578847 10.464912
AFFX-2315071 AA 0.001686 AA 0.807515 10.177494
AFFX-2315072 AA 0.006236 AA 0.763079 11.257955
AFFX-2315073 AB 0.002665 AB 0.119861 10.805366
AFFX-2315074 AB 0.010717 AB 0.103314 9.969567
AFFX-2315075 AB 0.006357 AB 0.118892 11.748671
AFFX-2315076 AB 0.003196 AB -0.007065 11.309094

Total number of rows: 238354

Table truncated, full table size 11215 Kbytes.

Supplementary file Size Download File type/resource
GSM672468_6932_Father_Sty.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM672468_6932_Father_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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