Whole-genome analysis of plasmodium spp. Utilizing a new agilent technologies DNA microarray platform

Heather Jill Painter Ponton, Lindsey M. Altenhofen, Björn F.C. Kafsack, Manuel Llinas

Research output: Chapter in Book/Report/Conference proceedingChapter

11 Citations (Scopus)

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.

Original languageEnglish (US)
Title of host publicationMalaria
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages213-219
Number of pages7
ISBN (Print)9781627030250
DOIs
StatePublished - Jan 1 2013

Publication series

NameMethods in Molecular Biology
Volume923
ISSN (Print)1064-3745

Fingerprint

Plasmodium
Oligonucleotide Array Sequence Analysis
Genome
Technology
Oligonucleotide Probes
Plasmodium falciparum
Genomics
Malaria
Parasites
Costs and Cost Analysis

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Painter Ponton, H. J., Altenhofen, L. M., Kafsack, B. F. C., & Llinas, M. (2013). Whole-genome analysis of plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. In Malaria: Methods and Protocols (pp. 213-219). (Methods in Molecular Biology; Vol. 923). Humana Press Inc.. https://doi.org/10.1007/978-1-62703-26-7_14
Painter Ponton, Heather Jill ; Altenhofen, Lindsey M. ; Kafsack, Björn F.C. ; Llinas, Manuel. / Whole-genome analysis of plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Malaria: Methods and Protocols. Humana Press Inc., 2013. pp. 213-219 (Methods in Molecular Biology).
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Painter Ponton, HJ, Altenhofen, LM, Kafsack, BFC & Llinas, M 2013, Whole-genome analysis of plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. in Malaria: Methods and Protocols. Methods in Molecular Biology, vol. 923, Humana Press Inc., pp. 213-219. https://doi.org/10.1007/978-1-62703-26-7_14

Whole-genome analysis of plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. / Painter Ponton, Heather Jill; Altenhofen, Lindsey M.; Kafsack, Björn F.C.; Llinas, Manuel.

Malaria: Methods and Protocols. Humana Press Inc., 2013. p. 213-219 (Methods in Molecular Biology; Vol. 923).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Painter Ponton HJ, Altenhofen LM, Kafsack BFC, Llinas M. Whole-genome analysis of plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. In Malaria: Methods and Protocols. Humana Press Inc. 2013. p. 213-219. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-62703-26-7_14