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Sample GSM672922 Query DataSets for GSM672922
Status Public on Feb 17, 2011
Title 9390_Mother (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 9390
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 0.000291 AB -0.115612 11.966773
AFFX-2315061 AB 0.003000 AB 0.103523 10.898333
AFFX-2315062 AB 0.053665 AB -0.199719 10.205069
AFFX-2315057 AB 0.007040 AB -0.040405 10.434277
AFFX-2315058 AA 0.007634 AA 0.798421 11.915325
AFFX-2315059 AB 0.002788 AB 0.260765 10.684088
AFFX-2315063 AA 0.000201 AA 0.808630 10.530107
AFFX-2315064 AA 0.011406 AA 0.708193 10.184497
AFFX-2315065 BB 0.011690 BB -0.509545 10.244813
AFFX-2315066 BB 0.006483 BB -0.675774 10.354309
AFFX-2315067 BB 0.000917 BB -0.599657 11.004671
AFFX-2315068 AA 0.009691 AA 0.835308 10.525594
AFFX-2315069 AB 0.016255 AB -0.040281 9.592738
AFFX-2315070 AB 0.003868 AB -0.064964 10.468797
AFFX-2315071 BB 0.001713 BB -0.845577 10.369786
AFFX-2315072 AA 0.003708 AA 0.739081 11.164349
AFFX-2315073 AA 0.011333 AA 0.807756 10.480738
AFFX-2315074 AB 0.080765 AB 0.234705 9.919936
AFFX-2315075 AA 0.040996 AA 0.633904 11.398732
AFFX-2315076 AA 0.010489 AA 0.670059 11.285726

Total number of rows: 238354

Table truncated, full table size 11208 Kbytes.

Supplementary file Size Download File type/resource
GSM672922_9390_Mother_Sty.CEL.gz 25.7 Mb (ftp)(http) CEL
GSM672922_9390_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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