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Sample GSM672454 Query DataSets for GSM672454
Status Public on Feb 17, 2011
Title 2332_Child_Mother (Mapping250_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: unaffected
tissue: peripheral blood
family: 2332
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 0.002223 AB -0.072039 12.021739
AFFX-2315061 BB 0.000261 BB -0.818377 10.847666
AFFX-2315062 AB 0.000380 AB -0.057623 10.320866
AFFX-2315057 BB 0.013659 BB -0.600531 10.461254
AFFX-2315058 AA 0.001670 AA 0.754730 11.970705
AFFX-2315059 AA 0.006700 AA 0.820010 10.748579
AFFX-2315063 AA 0.000217 AA 0.794897 10.552085
AFFX-2315064 AA 0.006897 AA 0.724269 10.060118
AFFX-2315065 AA 0.003193 AA 0.499713 10.228048
AFFX-2315066 BB 0.003343 BB -0.719670 10.406423
AFFX-2315067 AA 0.003765 AA 0.643269 11.279589
AFFX-2315068 AB 0.002241 AB 0.123270 10.577469
AFFX-2315069 AB 0.011630 AB -0.137606 9.653157
AFFX-2315070 AB 0.005707 AB -0.110482 10.363718
AFFX-2315071 BB 0.002870 BB -0.850589 10.397403
AFFX-2315072 AB 0.002106 AB 0.123279 11.226678
AFFX-2315073 AA 0.004011 AA 0.770827 10.682302
AFFX-2315074 AB 0.000562 AB 0.099623 9.818200
AFFX-2315075 AA 0.019852 AA 0.695919 11.606757
AFFX-2315076 BB 0.002627 BB -0.717358 11.068741

Total number of rows: 238354

Table truncated, full table size 11215 Kbytes.




Supplementary file Size Download File type/resource
GSM672454_2332_Mother_Sty.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM672454_2332_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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