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Sample GSM672897 Query DataSets for GSM672897
Status Public on Feb 17, 2011
Title 3519_Father (Mapping250K_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 3519
family member: Father
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 0.005027 AB -0.151797 11.927260
AFFX-2315061 AB 0.003668 AB 0.137448 11.167645
AFFX-2315062 BB 0.013838 BB -0.736457 10.425395
AFFX-2315057 AA 0.028883 AA 0.454822 10.221089
AFFX-2315058 AA 0.006260 AA 0.740708 11.920481
AFFX-2315059 AB 0.007500 AB 0.166249 10.684446
AFFX-2315063 AB 0.000764 AB -0.159221 10.921000
AFFX-2315064 BB 0.001942 BB -0.510561 9.958339
AFFX-2315065 AB 0.042856 AB -0.058381 10.160105
AFFX-2315066 BB 0.024630 BB -0.664836 10.248075
AFFX-2315067 AB 0.004463 AB 0.048388 11.099228
AFFX-2315068 AA 0.004425 AA 0.819906 10.595306
AFFX-2315069 AB 0.003457 AB -0.126989 9.756728
AFFX-2315070 AB 0.003934 AB -0.051595 10.272491
AFFX-2315071 BB 0.000337 BB -0.827077 10.361026
AFFX-2315072 AA 0.013794 AA 0.767816 11.027411
AFFX-2315073 AA 0.001719 AA 0.768971 10.582184
AFFX-2315074 AA 0.021727 AA 0.542673 9.673136
AFFX-2315075 AA 0.005509 AA 0.718361 11.572173
AFFX-2315076 AA 0.004594 AA 0.676838 11.077486

Total number of rows: 238354

Table truncated, full table size 11212 Kbytes.

Supplementary file Size Download File type/resource
GSM672897_3519_Father_Sty.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM672897_3519_Father_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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