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Sample GSM437639 Query DataSets for GSM437639
Status Public on Aug 08, 2009
Title Pseudoexfoliation syndrome pool - cohort 3
Sample type genomic
Source name Pseudoexfoliation syndrome - pool of 100 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 100 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
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
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
rs1000000-126_B_F_IFB1157714387:0 0.391
rs10000010-126_B_F_IFB1153208421:0 0.578
rs10000023-126_B_F_IFB1153358872:0 0.648
rs10000030-120_B_R_IFB1137703207:0 0.11
rs10000037-126_B_R_IFB1161100799:0 0.452
rs10000081-126_B_F_IFB1142608068:0 0.739
rs10000121-126_B_R_IFB1136471760:0 0.538
rs10000132-126_B_F_IFB1161100802:0 0.744
rs1000014-126_B_R_IFB1136184019:0 0.28
rs1000016-126_B_R_IFB1156563530:0 0.932
rs10000185-123_B_F_IFB1138742483:0 0.143
rs1000022-126_B_F_IFB1135126284:0 0.386
rs10000226-126_B_F_IFB1141217968:0 0.119
rs1000025-126_B_F_IFB1142595360:0 0.369
rs10000250-123_B_R_IFB1161282518:0 0.227
rs10000291-123_B_F_IFB1169496402:0 0.388
rs1000031-123_B_F_IFB1135583872:0 0.548
rs10000388-126_B_F_IFB1135932472:0 0.572
rs10000435-119_B_F_IFB1153036100:0 0.339
rs10000456-119_B_F_IFB1136722529:0 0.812

Total number of rows: 372550

Table truncated, full table size 14565 Kbytes.

Supplementary file Size Download File type/resource
GSM437639_raw_files.tar.gz 399.4 Mb (ftp)(http) TAR
Processed data included within Sample table
Processed data are available on Series record

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