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Sample GSM672848 Query DataSets for GSM672848
Status Public on Feb 17, 2011
Title 2714_Mother (Mapping250K_Nsp)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2714
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 AB 0.001176 AB -0.060974 12.140439
AFFX-2315061 BB 0.002990 BB -0.826433 11.131765
AFFX-2315062 AA 0.007709 AA 0.546787 10.761564
AFFX-2315057 BB 0.001440 BB -0.619736 10.987953
AFFX-2315058 AA 0.004986 AA 0.708766 11.623605
AFFX-2315059 AA 0.000542 AA 0.758678 10.631261
AFFX-2315063 BB 0.001227 BB -0.717208 11.074221
AFFX-2315064 BB 0.005706 BB -0.672949 10.924532
AFFX-2315065 BB 0.067444 BB -0.405286 10.586518
AFFX-2315066 BB 0.004064 BB -0.672672 10.764924
AFFX-2315067 BB 0.029744 BB -0.533666 11.039936
AFFX-2315068 BB 0.003650 BB -0.681727 10.724491
AFFX-2315069 AB 0.005026 AB -0.063401 10.764843
AFFX-2315070 BB 0.029706 BB -0.743183 10.747781
AFFX-2315071 BB 0.009069 BB -0.747187 9.994020
AFFX-2315072 AA 0.016544 AA 0.574644 10.912029
AFFX-2315073 BB 0.005594 BB -0.628527 10.735114
AFFX-2315074 AB 0.006175 AB 0.096742 10.597569
AFFX-2315075 AB 0.001205 AB 0.147253 11.726012
AFFX-2315076 BB 0.005775 BB -0.509896 10.871942

Total number of rows: 262314

Table truncated, full table size 12381 Kbytes.

Supplementary file Size Download File type/resource
GSM672848_2714_Mother_Nsp.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM672848_2714_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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