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Sample GSM672926 Query DataSets for GSM672926
Status Public on Feb 17, 2011
Title 3921_Mother (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 3921
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 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 AA 0.034986 AA 0.593141 11.926775
AFFX-2315061 AB 0.007993 AB 0.043394 11.111485
AFFX-2315062 AA 0.013080 AA 0.586908 10.471365
AFFX-2315057 BB 0.021515 BB -0.671403 10.925858
AFFX-2315058 AA 0.063891 AA 0.663070 11.457392
AFFX-2315059 AB 0.011477 AB 0.218004 10.568534
AFFX-2315063 AB 0.012421 AB -0.141316 10.901443
AFFX-2315064 AB 0.014721 AB 0.147091 10.916415
AFFX-2315065 BB 0.000224 BB -0.469164 10.320475
AFFX-2315066 AB 0.035840 AB 0.007006 10.714540
AFFX-2315067 AA 0.156630 AA 0.402001 10.986329
AFFX-2315068 AB 0.043950 AB 0.252522 10.950933
AFFX-2315069 BB 0.012820 BB -0.853829 10.763341
AFFX-2315070 BB 0.064265 BB -0.775504 10.504991
AFFX-2315071 AB 0.007648 AB -0.131798 9.920950
AFFX-2315072 AB 0.012829 AB -0.008016 10.613845
AFFX-2315073 AB 0.010638 AB 0.126048 10.770336
AFFX-2315074 BB 0.005238 BB -0.596983 10.347012
AFFX-2315075 AA 0.014462 AA 0.651842 11.425699
AFFX-2315076 AB 0.034740 AB -0.060038 10.743382

Total number of rows: 262314

Table truncated, full table size 12368 Kbytes.

Supplementary file Size Download File type/resource
GSM672926_3921_Mother_Nsp.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM672926_3921_Mother_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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