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Title: A systematic spatial bias in microarray hybridizations caused by probe spot position-dependent variability in lateral diffusion      
dateReleased:
12-22-2010
description:
The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay format for high-throughput detection of many parallel targetsin medical and biological research. Though commonly applied, microarray technology still suffers limitations arising from problems of data robustness and reproducibility across platforms, stemming in part from an incomplete understanding of the complex processes governing surface hybridization behavior. It has been observed that there are non-random spatial variations within individual microarray hybridizations, but the causative mechanisms of positional bias remain largely unexplained. This study identifies a symptomatic spatial bias in surface hybridization signal intensitywith systematically increased signal intensities of spots located at the boundaries of the spotted areas of the microarray slide and characterizes the underlying mechanistic principle of this bias using a simplified block array format. Experimentally-derived hybridization dynamics are compared with a mathematical modeling analysis, which together showthat the driver of the spatial bias is a position-dependent variation in lateral diffusion. Numerical simulations employing a diffusion-based model are used to demonstrate the strong influence of microarray well geometry on this spatial bias and to determine optimal conditions for which this bias can be minimized or eliminated, resulting in increased uniformity of microarray hybridization. A simplified square array of 900 identical spotted probes was hybridized using different target concentrations and different time periods to analyze systematically spatial biases in microarray hybridizations.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-26275
refinement:
raw
alternateIdentifiers:
26275
keywords:
functional genomics
dateModified:
05-02-2014
availability:
available
types:
gene expression
name:
Desulfovibrio halophilus
ID:
A-GEOD-11310
name:
DOME_Dsv.halophilus_900_v1
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26275/E-GEOD-26275.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-26275/E-GEOD-26275.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26275
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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