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Sample GSM437637 Query DataSets for GSM437637
Status Public on Aug 08, 2009
Title Age-related macular degeneration pool - cohort 2
Sample type genomic
 
Source name Age-related macular degeneration - pool of 131 individuals
Organism Homo sapiens
Characteristics tissue: blood
Extracted molecule genomic DNA
Extraction protocol Blood samples from individuals from each phenotype definition were pooled. A single extraction was performed on each blood pool. Extraction was done according to manufacturers guidelines using the QIA-AMP DNA blood maxi kit (QIAGEN, Valencia, CA, USA). The extracted DNA was quantified by spectrophotometry.
Label Cy3, Cy5
Label protocol The Infinium assay used on the Illumina arrays is based on allele-specific single base extension using two color labeling with the Cy3 and Cy5 fluorescent dyes
 
Hybridization protocol Array data. SNPs were genotyped on pool samples using Illumina arrays. Arrays were treated according to standard protocols.
Scan protocol Arrays were scanned at Queensland Institute of Medical Research.
Description Pool of 131 individuals
Data processing Raw probe intensities were dumped from Illumina array software and analysed using methods described in Macgregor et al Nucleic Acids Research, 2006, Vol. 34, No. 7 e55.
Bead-level intensity data were analyzed. SNPs with beadscore values <-50 were excluded. Copy number variants and SNPs from the sex chromosomes were not analyzed. SNPs were also removed in the initial quality control if they had a minor allele frequency <1% in the HapMap CEU reference samples. SNPs from Illumina TOP strand exhibited different levels of pooling error to SNPs from Illumina BOTTOM strand, hence only 261887 (HumanHap550) and 375246 (1M) SNPs from the ‘BOTTOM’ strand are included in the final analysis (in estimated pooling frequencies).
 
Submission date Aug 07, 2009
Last update date Aug 07, 2009
Contact name Stuart Macgregor
E-mail(s) stuart.macgregor@qimr.edu.au
Organization name Queensland Institute of Medical Research
Department Genetic Epidemiology
Street address 300 Herston Road
City Brisbane
State/province Queensland
ZIP/Postal code 4029
Country Australia
 
Platform ID GPL6983
Series (1)
GSE17557 Blood pooling experiments on ophthalmalogic phenotypes with Illumina arrays

Data table header descriptions
ID_REF
VALUE Estimate of allele frequency for the pool based on the raw data from all arrays. The estimate of pooling allele frequency (PAF) comes from PAF=R/(R+G) where R and G are the red and green intensities respectively. The PAFs were normalized to ensure that the mean allele frequency was 0.5 over each 'stripe' of the array.

Data table
ID_REF VALUE
rs1000000-126_B_F_IFB1157714387:0 0.379
rs10000010-126_B_F_IFB1153208421:0 0.524
rs10000023-126_B_F_IFB1153358872:0 0.614
rs10000030-120_B_R_IFB1137703207:0 0.076
rs10000037-126_B_R_IFB1161100799:0 0.386
rs10000081-126_B_F_IFB1142608068:0 0.739
rs10000121-126_B_R_IFB1136471760:0 0.471
rs10000132-126_B_F_IFB1161100802:0 0.77
rs1000014-126_B_R_IFB1136184019:0 0.291
rs1000016-126_B_R_IFB1156563530:0 0.915
rs10000185-123_B_F_IFB1138742483:0 0.188
rs1000022-126_B_F_IFB1135126284:0 0.462
rs10000226-126_B_F_IFB1141217968:0 0.14
rs1000025-126_B_F_IFB1142595360:0 0.336
rs10000250-123_B_R_IFB1161282518:0 0.144
rs10000291-123_B_F_IFB1169496402:0 0.318
rs1000031-123_B_F_IFB1135583872:0 0.503
rs1000032-126_B_R_IFB1136145093:0 0.141
rs10000388-126_B_F_IFB1135932472:0 0.632
rs10000435-119_B_F_IFB1153036100:0 0.271

Total number of rows: 375246

Table truncated, full table size 14670 Kbytes.




Supplementary file Size Download File type/resource
GSM437637_raw_files.tar.gz 199.7 Mb (ftp)(http) TAR
Processed data included within Sample table
Processed data are available on Series record
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