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Sample GSM672898 Query DataSets for GSM672898
Status Public on Feb 17, 2011
Title 3519_Mother (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 3519
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 AB 0.014389 AB -0.181727 12.004773
AFFX-2315061 AB 0.000885 AB 0.118907 11.081617
AFFX-2315062 BB 0.001863 BB -0.679567 10.238938
AFFX-2315057 BB 0.015458 BB -0.596544 10.432467
AFFX-2315058 AA 0.009918 AA 0.738645 11.882902
AFFX-2315059 BB 0.000846 BB -0.735972 10.544428
AFFX-2315063 AA 0.002685 AA 0.797633 10.644150
AFFX-2315064 AB 0.075291 AB 0.356406 10.113729
AFFX-2315065 AB 0.082511 AB -0.165816 10.306758
AFFX-2315066 AB 0.004545 AB -0.140052 10.277286
AFFX-2315067 AB 0.003898 AB 0.079695 11.143267
AFFX-2315068 AB 0.002304 AB 0.165409 10.644358
AFFX-2315069 AB 0.009724 AB -0.152348 9.700480
AFFX-2315070 AB 0.000613 AB -0.057126 10.331717
AFFX-2315071 AA 0.003011 AA 0.786148 10.265371
AFFX-2315072 AA 0.008025 AA 0.782980 11.117580
AFFX-2315073 AB 0.000660 AB 0.139326 10.646911
AFFX-2315074 BB 0.027948 BB -0.499404 9.692617
AFFX-2315075 AB 0.014722 AB 0.041197 11.862475
AFFX-2315076 AA 0.002802 AA 0.624861 11.114121

Total number of rows: 238354

Table truncated, full table size 11209 Kbytes.

Supplementary file Size Download File type/resource
GSM672898_3519_Mother_Sty.CEL.gz 26.0 Mb (ftp)(http) CEL
GSM672898_3519_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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