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Sample GSM672475 Query DataSets for GSM672475
Status Public on Feb 17, 2011
Title 8135_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8135
family member: Mother
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 0.000889 BB -0.750369 11.912951
AFFX-2315061 AB 0.008967 AB 0.139609 11.257455
AFFX-2315062 AB 0.019552 AB -0.079471 10.107360
AFFX-2315057 BB 0.037653 BB -0.490602 10.289176
AFFX-2315058 AA 0.087128 AA 0.685744 11.736678
AFFX-2315059 AB 0.017271 AB 0.152784 10.575045
AFFX-2315063 AB 0.003148 AB -0.172381 10.749960
AFFX-2315064 AB 0.173032 AB 0.293560 9.740026
AFFX-2315065 AA 0.042188 AA 0.499236 9.997779
AFFX-2315066 BB 0.129847 BB -0.696092 10.001308
AFFX-2315067 AB 0.007138 AB 0.074489 11.095684
AFFX-2315068 AA 0.046739 AA 0.796215 10.317382
AFFX-2315069 AA 0.000050 AA 0.696679 9.798104
AFFX-2315070 AA 0.032790 AA 0.472889 10.108699
AFFX-2315071 AB 0.012290 AB -0.127653 10.014851
AFFX-2315072 AA 0.055059 AA 0.727243 10.850668
AFFX-2315073 AA 0.029660 AA 0.747090 10.329372
AFFX-2315074 BB 0.091614 BB -0.386525 9.632619
AFFX-2315075 AB 0.005449 AB 0.011361 11.640066
AFFX-2315076 BB 0.032177 BB -0.678799 10.793462

Total number of rows: 238354

Table truncated, full table size 11220 Kbytes.

Supplementary file Size Download File type/resource
GSM672475_8135_Mother_Sty.CEL.gz 26.9 Mb (ftp)(http) CEL
GSM672475_8135_Mother_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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