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Sample GSM672456 Query DataSets for GSM672456
Status Public on Feb 17, 2011
Title 2377_Child_Father (Mapping250_Sty)
Sample type genomic
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2377
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 0.000538 AB -0.112318 11.930698
AFFX-2315061 BB 0.001186 BB -0.817212 10.787026
AFFX-2315062 AB 0.000552 AB -0.073388 10.395101
AFFX-2315057 AA 0.005959 AA 0.540715 10.294478
AFFX-2315058 AA 0.008497 AA 0.780290 11.868793
AFFX-2315059 AA 0.005368 AA 0.850449 10.838673
AFFX-2315063 AA 0.005625 AA 0.837925 10.471708
AFFX-2315064 AB 0.031265 AB 0.314202 10.187147
AFFX-2315065 AB 0.034942 AB -0.139334 10.337112
AFFX-2315066 BB 0.018882 BB -0.748082 10.406520
AFFX-2315067 AB 0.003974 AB 0.017351 11.253330
AFFX-2315068 AB 0.002274 AB 0.071979 10.755082
AFFX-2315069 AB 0.011197 AB -0.006849 9.760615
AFFX-2315070 BB 0.015808 BB -0.657066 10.464190
AFFX-2315071 BB 0.000479 BB -0.835190 10.358621
AFFX-2315072 AB 0.000635 AB 0.092073 11.233365
AFFX-2315073 AA 0.001679 AA 0.803244 10.654256
AFFX-2315074 BB 0.015507 BB -0.570910 9.919929
AFFX-2315075 AA 0.011490 AA 0.793133 11.570855
AFFX-2315076 BB 0.006080 BB -0.719592 11.234590

Total number of rows: 238354

Table truncated, full table size 11219 Kbytes.

Supplementary file Size Download File type/resource
GSM672456_2377_Father_Sty.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM672456_2377_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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