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Sample GSM670864 Query DataSets for GSM670864
Status Public on Feb 17, 2011
Title 2894_Child (GenomeWideSNP_6)
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
tissue: peripheral blood
phenotype: idiopathic MR
family: 2894
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 identified using the Genotyping Console 3.0.1 program.
Since this program cannot perform pair-wise comparisons, we compared the results of each sample to a reference dataset generated by the combined results for the 30 parents in the 15 trios studied on the platform.
 
Submission date Feb 08, 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 GPL6801
Series (2)
GSE27145 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (GenomeWideSNP_6)
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
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.003097 BB 590.350037 3234.968506
SNP_A-1967418 BB 0.001843 BB 254.178131 635.634766
SNP_A-1969580 BB 0.006698 BB 865.750671 3446.993408
SNP_A-4263484 AB 0.004664 AB 1336.385864 992.030457
SNP_A-1978185 AA 0.005594 AA 1742.088623 268.905090
SNP_A-4264431 AA 0.015799 AA 1449.567871 318.013702
SNP_A-1980898 AA 0.003119 AA 981.926697 243.499985
SNP_A-1983139 AA 0.001666 AA 2927.656738 709.271729
SNP_A-4265735 AB 0.006017 AB 718.339966 794.504028
SNP_A-1995832 AA 0.002122 AA 2145.853516 309.398865
SNP_A-1995893 AA 0.008805 AA 2587.708984 1026.484863
SNP_A-1997689 BB 0.001171 BB 631.592529 3169.639404
SNP_A-1997709 AA 0.004613 AA 2442.218994 261.041077
SNP_A-1997896 AA 0.010326 AA 1094.338501 531.000061
SNP_A-1997922 AA 0.000842 AA 828.490479 222.835510
SNP_A-2000230 AA 0.001152 AA 2681.942383 1179.710938
SNP_A-2000332 BB 0.005083 BB 1079.912476 3213.945801
SNP_A-2000337 AA 0.003200 AA 1957.110229 272.880554
SNP_A-2000342 AA 0.001272 AA 3130.844238 827.292542
SNP_A-4268173 AA 0.001849 AA 1317.727417 260.032288

Total number of rows: 909622

Table truncated, full table size 46107 Kbytes.




Supplementary file Size Download File type/resource
GSM670864_2894_Child.CEL.gz 29.1 Mb (ftp)(http) CEL
GSM670864_2894_Child.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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