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Expression Profiling the Schizont and Trophozoite Stages of Plasmodium falciparum with a Long Oligonucleotide Microarray

Zbynek Bozdech, Jingchun Zhu, Brian Pulliam, Marcin Joachimiak, Fred Cohen, and Joseph DeRisi

We developed a software package, ArrayOligoSelector, to design an open reading frame 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 6000 open reading frames of the P. falciparum genome was constructed. An additional set of oligonucleotides is designed using an improved version of the program and more recent genome sequnces up to October 2001. Array performance was evaluated through the use of control oligonucleotides harboring a series of mutations, as well as traditional Northern blotting. Using this array, we extensively characterized the gene expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes respective to these two stages.

From this web site you can access the oligonucleotide sequences, our open reading frame predictions, ArrayOligoSelector program, and data from the microarray experiments.

Oligo Sequences:

Open Reading Frame Predictions: We have performed the first in-house P. falciparum gene predictions using the contig sequences available in August 2000 and the GlimmerM software.  Based on this prediction, we have designed our first set of 70mer oligonucleotides.  Upon a more recent release of contig sequences from the genome centers, we have subsequently performed a second in-house gene prediction in October 2000.  Our oligonucleotides were mapped to the second in-house predictions as well.

Oligos' Gene Targets:

Software Program:

Microarray Experiments:

  1. Six microarray experiments used to generate the clustering results in Figure 2

  2. Besides the abover six experiments, additional ten microarray experiments are performed to generate Figure 3 and 4.

  3. Nine microarray experiments comparing PCR fragments of control yesat intergenic regions with malaria total RNA