Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.docVIP

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Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.doc

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Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray

Open Access Research Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray Zbynek Bozdech*, Jingchun Zhu*, Marcin P Joachimiak?, Fred E Cohen?, Brian Pulliam* and Joseph L DeRisi* Addresses: *Department of Biochemistry and Biophysics, and ?Department of Molecular and Cellular Pharmacology, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143-0448, USA. Correspondence: Joseph L DeRisi. E-mail: joe@ Published: 31 January 2003 Received: 23 August 2002 Revised: 10 October 2002 Accepted: 5 December 2002 Genome Biology 2003, 4:R9 The electronic version of this article is the complete one and can be found online at /2003/4/2/R9 ? 2003 Bozdech et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the articles original URL. Abstract Background: The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development. Results: We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3 ?end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as t