Malaria pp 213-219 | Cite as

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

  • Heather J. Painter
  • Lindsey M. Altenhofen
  • Björn F. C. Kafsack
  • Manuel Llinás
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 923)

Abstract

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.

Key words DNA microarray Plasmodium genomics Microarray hybridization Transcription profiling Gene expression Comparative genomic hybridization Agilent Technologies 

References

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Heather J. Painter
    • 1
  • Lindsey M. Altenhofen
    • 1
  • Björn F. C. Kafsack
    • 1
  • Manuel Llinás
    • 1
  1. 1.Lewis-Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonUSA

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