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Sample GSM670861 Query DataSets for GSM670861
Status Public on Feb 17, 2011
Title 2569_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: 2569
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 0.004020 BB 754.413452 3693.383301
SNP_A-1967418 BB 0.002733 BB 216.905060 667.602905
SNP_A-1969580 BB 0.004956 BB 900.652710 3183.097656
SNP_A-4263484 BB 0.006527 BB 440.965637 1789.490845
SNP_A-1978185 AA 0.001614 AA 1737.679321 315.279663
SNP_A-4264431 AA 0.004841 AA 1427.982300 281.852722
SNP_A-1980898 BB 0.002832 BB 202.478577 852.601318
SNP_A-1983139 AA 0.022244 AA 2976.916992 952.012390
SNP_A-4265735 AB 0.001079 AB 811.180420 903.646240
SNP_A-1995832 AB 0.002277 AB 1519.333862 1040.737061
SNP_A-1995893 AB 0.003399 AB 1453.649536 1714.005249
SNP_A-1997689 BB 0.002414 BB 631.664246 3279.639404
SNP_A-1997709 AA 0.001602 AA 2058.228271 241.433105
SNP_A-1997896 AB 0.005255 AB 923.570557 1413.904663
SNP_A-1997922 AA 0.004110 AA 951.026306 216.596634
SNP_A-2000230 AA 0.011506 AA 2328.776611 1211.865601
SNP_A-2000332 BB 0.005083 BB 860.653931 3074.766357
SNP_A-2000337 AA 0.005068 AA 1645.563110 303.142151
SNP_A-2000342 AA 0.005501 AA 2916.526611 833.099731
SNP_A-4268173 AA 0.008890 AA 1298.762085 306.599091

Total number of rows: 909622

Table truncated, full table size 46106 Kbytes.




Supplementary file Size Download File type/resource
GSM670861_2569_Child.CEL.gz 29.4 Mb (ftp)(http) CEL
GSM670861_2569_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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