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Sample GSM672890 Query DataSets for GSM672890
Status Public on Feb 17, 2011
Title 2714_Child (Mapping250K_Sty)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 2714
family member: Child
gender: Male
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 BB 0.003763 BB -0.714132 12.311855
AFFX-2315061 AB 0.002859 AB 0.139070 11.841936
AFFX-2315062 AA 0.049898 AA 0.644446 10.645681
AFFX-2315057 BB 0.092670 BB -0.483377 10.885500
AFFX-2315058 AA 0.005569 AA 0.705843 12.170661
AFFX-2315059 AB 0.006814 AB 0.292891 10.918433
AFFX-2315063 AB 0.005043 AB -0.081338 11.064050
AFFX-2315064 BB 0.010807 BB -0.321888 10.058771
AFFX-2315065 BB 0.002683 BB -0.454922 10.568294
AFFX-2315066 AB 0.031983 AB 0.093462 10.581480
AFFX-2315067 BB 0.028382 BB -0.629120 11.250431
AFFX-2315068 BB 0.001684 BB -0.752114 10.745256
AFFX-2315069 AB 0.006122 AB -0.136781 10.213915
AFFX-2315070 BB 0.005957 BB -0.529793 10.547603
AFFX-2315071 BB 0.001373 BB -0.803374 10.349809
AFFX-2315072 AA 0.064101 AA 0.721502 11.231538
AFFX-2315073 AB 0.000713 AB 0.133112 10.629918
AFFX-2315074 BB 0.007640 BB -0.389224 10.036556
AFFX-2315075 AA 0.029222 AA 0.720858 11.813967
AFFX-2315076 BB 0.011982 BB -0.640547 11.232539

Total number of rows: 238354

Table truncated, full table size 11257 Kbytes.




Supplementary file Size Download File type/resource
GSM672890_2714_Child_Sty.CEL.gz 26.8 Mb (ftp)(http) CEL
GSM672890_2714_Child_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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