Abstract
BackgroundMicroarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic.ResultsWe have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.ConclusionSimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from .
Highlights
Microarrays were first developed to assess gene expression but are used to map protein-binding sites and to assess allelic variation between individuals
We have addressed the current lack of such microarray design tools by developing SimArray, a user-friendly and user-configurable program that generates a randomised spot layout, computes the maximum meta-grid area, and estimates printing time, in response to user-defined design decisions
We have developed a user-friendly microarray design tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and an estimated print time, in response to user-specified design decisions
Summary
Microarrays were first developed to assess gene expression but are used to map protein-binding sites and to assess allelic variation between individuals. Whole-genome arrays, typically composed of tiled gDNA or oligonucleotides [6], have been used to identify in vivo sites of protein-DNA interactions [7,8] or allelic variation [9,10]. Whilst these applications dominate, other formats, for example antibody arrays, facilitate analysis of protein and small-molecule analytes [11,12].
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