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Sample GSM672481 Query DataSets for GSM672481
Status Public on Feb 17, 2011
Title 8327_Child_Mother (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 8327
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 0.005433 AB -0.149663 11.903742
AFFX-2315061 AA 0.001200 AA 0.876072 10.908189
AFFX-2315062 AA 0.001370 AA 0.654842 10.142114
AFFX-2315057 AB 0.009577 AB -0.039309 10.608445
AFFX-2315058 AA 0.033762 AA 0.828059 11.838539
AFFX-2315059 AB 0.028367 AB 0.337847 10.696158
AFFX-2315063 AA 0.006808 AA 0.755526 10.429399
AFFX-2315064 AB 0.010426 AB 0.252118 10.008387
AFFX-2315065 AA 0.013590 AA 0.420581 10.191322
AFFX-2315066 BB 0.000759 BB -0.696391 10.431100
AFFX-2315067 BB 0.028064 BB -0.633597 10.795573
AFFX-2315068 AA 0.003231 AA 0.841063 10.601618
AFFX-2315069 BB 0.049397 BB -0.664624 9.762520
AFFX-2315070 BB 0.005799 BB -0.580082 10.436794
AFFX-2315071 AA 0.004528 AA 0.744335 9.981793
AFFX-2315072 AA 0.002153 AA 0.741876 11.149813
AFFX-2315073 AB 0.010940 AB 0.100510 10.405390
AFFX-2315074 AB 0.023485 AB 0.178960 9.814188
AFFX-2315075 AA 0.002460 AA 0.749771 11.474097
AFFX-2315076 BB 0.005285 BB -0.735579 11.159715

Total number of rows: 238354

Table truncated, full table size 11215 Kbytes.

Supplementary file Size Download File type/resource
GSM672481_8327_Mother_Sty.CEL.gz 24.9 Mb (ftp)(http) CEL
GSM672481_8327_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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