| Summary: | <p><b>Abstract</b></p> <p><b>Background</b></p> <p>DNA microarrays have been a valuable tool in malaria research for over a decade but remain in limited use in part due their relatively high cost, poor availability, and technical difficulty. With the aim of alleviating some of these factors next-generation DNA microarrays for genome-wide transcriptome analysis for both <it>Plasmodium falciparum</it> and <it>Plasmodium berghei</it> using the Agilent 8x15K platform were designed.</p> <p><b>Methods</b></p> <p>Probe design was adapted from previously published methods and based on the most current transcript predictions available at the time for <it>P. falciparum</it> or <it>P. berghei</it>. Array performance and transcriptome analysis was determined using dye-coupled, aminoallyl-labelled cDNA and streamlined methods for hybridization, washing, and array analysis were developed.</p> <p><b>Results</b></p> <p>The new array design marks a notable improvement in the number of transcripts covered and average number of probes per transcript. Array performance was excellent across a wide range of transcript abundance, with low inter-array and inter-probe variability for relative abundance measurements and it recapitulated previously observed transcriptional patterns. Additionally, improvements in sensitivity permitted a 20-fold reduction in necessary starting RNA amounts, further reducing experimental costs and widening the range of application.</p> <p><b>Conclusions</b></p> <p>DNA microarrays utilizing the Agilent 8x15K platform for genome-wide transcript analysis in <it>P. falciparum</it> and <it>P. berghei</it> mark an improvement in coverage and sensitivity, increased availability to the research community, and simplification of the experimental methods.</p>
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