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Sample GSM672471 Query DataSets for GSM672471
Status Public on Feb 17, 2011
Title 6942_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 6942
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 AB 0.016121 AB -0.149378 12.136133
AFFX-2315061 AB 0.008085 AB 0.125760 11.250273
AFFX-2315062 AA 0.039112 AA 0.653863 10.487405
AFFX-2315057 BB 0.010362 BB -0.562154 10.629390
AFFX-2315058 AB 0.005658 AB 0.097170 12.014015
AFFX-2315059 AA 0.002284 AA 0.820417 10.790783
AFFX-2315063 AA 0.001477 AA 0.788969 10.593773
AFFX-2315064 AA 0.008810 AA 0.682928 9.993290
AFFX-2315065 AB 0.040458 AB -0.121564 10.541914
AFFX-2315066 BB 0.036593 BB -0.684763 10.583142
AFFX-2315067 AB 0.020035 AB -0.057511 11.211116
AFFX-2315068 AB 0.003772 AB 0.092774 10.890366
AFFX-2315069 AB 0.015716 AB -0.019933 9.627481
AFFX-2315070 AB 0.026702 AB -0.146995 10.220484
AFFX-2315071 AB 0.002104 AB -0.193681 10.416841
AFFX-2315072 BB 0.006747 BB -0.764451 11.223573
AFFX-2315073 AB 0.001658 AB 0.118041 10.777191
AFFX-2315074 BB 0.074616 BB -0.389009 9.702615
AFFX-2315075 AA 0.088872 AA 0.679334 11.762258
AFFX-2315076 BB 0.027881 BB -0.664527 11.284717

Total number of rows: 238354

Table truncated, full table size 11206 Kbytes.

Supplementary file Size Download File type/resource
GSM672471_6942_Father_Sty.CEL.gz 26.1 Mb (ftp)(http) CEL
GSM672471_6942_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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