Whole-Genome Analysis of Plasmodium spp. Utilizing a New Agilent Technologies DNA Microarray Platform

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
Methods in molecular biology (Clifton, N.J.) (Impact Factor: 1.29). 01/2013; 923:213-9. DOI: 10.1007/978-1-62703-026-7_14
Source: PubMed


The application of DNA microarray technologies to malaria genomics has been widely used but has been limited by sample availability and technical variability. To address these issues, we present a microarray hybridization protocol that has been optimized for use with two new Agilent Technologies DNA microarrays for Plasmodium falciparum and P. berghei. Using the most recent genome sequences available for each species, we have designed ∼14,000 oligonucleotide probes representing ∼5,600 transcripts for each species. Included in each array design are numerous probes that allow for the identification of parasite developmental stages, common Plasmodium molecular markers used in genetic manipulation, and manufacturer probes that control for array consistency and quality. Overall, the Agilent Plasmodium spp. array designs and hybridization methodology provides a sensitive, easy-to-use, high-quality, cost-effective alternative to other currently available microarray platforms.

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Available from: Heather J Painter, Jan 09, 2016
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    • "The genome of Plasmodium falciparum is a chimera of two eukaryotes and two prokaryotes currently housed on 14 nuclear chromosomes, a 6 kb reduced mitochondrial genome, and a 35 kb apicoplast genome (Gardner et al. 2002). Publication of the P. falciparum strain 3D7 genome in 2002 allowed parasitologists to accelerate the task of assigning function to the ~5,600 genes (Painter et al. 2013). Postgenomic studies indicate that only ~8% of P. falciparum genes are involved in metabolism compared to 17% of the ~6,000 genes in Saccharomyces cerevisiae (Goffeau et al. 1996). "
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    • "Parasite RNA was isolated at four specific time points (6–14 hpi, 16–24 hpi, 26–34 hpi & 36–44 hpi) from synchronized SEMP1-DD parasites cultured with and without Shield. The Cy5-labelled SEMP1-DD cRNA was mixed with an equal amount of Cy3-labelled 3D7 reference cRNA (mixed stages) and hybridized onto an Agilent P. falciparum Microarray slide (AMADID #037237) containing oligonucleotides for all P. falciparum genes [19]. We did not detect any significant transcriptional changes in SEMP1-depleted parasites using Significance Analysis for Microarrays [20]. "
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