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Sample GSM676378 Query DataSets for GSM676378
Status Public on Feb 17, 2011
Title 5993_Child (Illumina HumanHap550)
Sample type genomic
 
Source name 5993_Child
Organism Homo sapiens
Characteristics developmental state: Developmental Delay
family: 5993
phenotype: idiopathic MR
gender: Male
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from blood samples using the Puregene DNA kit
Label C-Bio and A-DNP
Label protocol DNA from the proband in each trio was used for hybridization on the Illumina Human Hap550 Beadchips according to the manufacturer’s instructions
 
Hybridization protocol DNA was hybridized overnight to a Beadchip placed in a humidified chamber
Scan protocol Beadchips were imaged using a two-color confocal laser system with 0.8-μm resolution to identify both SNP alleles
Data processing The intensities for each allele were extracted and normalized, and values for genotypes, allelic ratio (B-allele frequency) and logR ratio were calculated using an Illumina-supplied cluster file, which is based on a set of about 100 HapMap reference samples. The normalization algorithm adjusts for nominal offset, cross-talk, and intensity variations observed in the two-color channels. CNV detection was done using PennCNV [20] with a threshold of 5 SNP-minimum per bin
 
Submission date Feb 16, 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 GPL6433
Series (2)
GSE27364 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Illumina HumanHap550)
GSE27367 Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR

Data table header descriptions
ID_REF
VALUE G Type
5993_Child.Score
5993_Child.R
5993_Child.Theta
5993_Child.B Allele Freq
5993_Child.Log R Ratio

Data table
ID_REF VALUE 5993_Child.Score 5993_Child.R 5993_Child.Theta 5993_Child.B Allele Freq 5993_Child.Log R Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3069536 3.262061 0.007133224 0.00 -0.5826557
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.6703396 3.035204 0.0331806 0.00 -0.5594191
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.2845602 3.386685 0.02328039 0.00 -0.4743762
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3254292 4.625405 0.04569182 0.03113416 -0.4346757
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2503389 3.336275 0.05119281 0.00 -0.4878391
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.199644 3.27265 0.08961083 0.06809646 -0.4152657
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.2597956 1.242728 0.07275929 0.01488335 -0.5590063
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2554387 4.18996 0.01994526 0.02598824 -1.067725
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.1791639 0.4908141 0.06038155 0.01238778 -1.644055
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.2740649 2.273183 0.01844113 0.00 -0.3846087
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.3202845 1.727181 0.02716944 0.007457022 -0.4242615
MitoA14906G-13273310_B_R_IFB1141671343:0 BB 0.3634304 3.758727 0.8045797 1 0.4563722
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2522812 4.151375 0.06051924 0.05333152 -0.4111075
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.2818599 3.036588 0.03137324 0.00 -0.4079643
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2571433 2.801975 0.9586336 1 0.09164538
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.2790043 4.31778 0.01175451 0.00 -0.4457368
MitoA15908G-13273317_B_R_IFB1141698995:0 AA 0.3015448 4.399357 0.01860271 0.00 -0.2651729
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.3240124 2.965435 0.02375069 0.00 -0.6388258
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.4755262 3.482318 0.07026541 0.00 -0.5198866
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3252551 2.483634 0.02116389 0.00 -0.5339602

Total number of rows: 555352

Table truncated, full table size 45662 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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