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Sample GSM672892 Query DataSets for GSM672892
Status Public on Feb 17, 2011
Title 2714_Mother (Mapping250K_Sty)
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
E-mail(s) tbtucker@interchange.ubc.ca
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
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
CONTRAST
STRENGTH

Data table
ID_REF VALUE CONFIDENCE FORCED CALL CONTRAST STRENGTH
AFFX-2315060 AB 0.000044 AB -0.124197 12.344671
AFFX-2315061 BB 0.002938 BB -0.750164 11.575621
AFFX-2315062 AA 0.014922 AA 0.620187 10.449415
AFFX-2315057 BB 0.067452 BB -0.550322 10.706818
AFFX-2315058 AA 0.006272 AA 0.671065 12.237197
AFFX-2315059 AA 0.015819 AA 0.815965 10.866550
AFFX-2315063 BB 0.035861 BB -0.758130 11.207274
AFFX-2315064 BB 0.018006 BB -0.371236 10.174133
AFFX-2315065 BB 0.058875 BB -0.377834 10.661875
AFFX-2315066 BB 0.007574 BB -0.627696 10.588573
AFFX-2315067 BB 0.007049 BB -0.592003 11.242323
AFFX-2315068 BB 0.001465 BB -0.745853 10.791178
AFFX-2315069 AB 0.005644 AB -0.127583 10.223976
AFFX-2315070 BB 0.025542 BB -0.477924 10.581481
AFFX-2315071 BB 0.003983 BB -0.811592 10.348635
AFFX-2315072 AA 0.021077 AA 0.663700 11.123347
AFFX-2315073 BB 0.000696 BB -0.629535 10.466794
AFFX-2315074 AB 0.000465 AB 0.132537 9.966622
AFFX-2315075 AB 0.059439 AB -0.008897 11.991406
AFFX-2315076 BB 0.003697 BB -0.608278 11.153374

Total number of rows: 238354

Table truncated, full table size 11252 Kbytes.




Supplementary file Size Download File type/resource
GSM672892_2714_Mother_Sty.CEL.gz 26.2 Mb (ftp)(http) CEL
GSM672892_2714_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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