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New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community.

TitleNew Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community.
Publication TypeJournal Article
Year of Publication2012
AuthorsKafsack BFC, Painter HJ, LlinĂ¡s M
JournalMalar J
Volume11
Pagination187
Date Published2012 Jun 08
ISSN1475-2875
KeywordsGene Expression Profiling, Oligonucleotide Array Sequence Analysis, Parasitology, Plasmodium berghei, Plasmodium falciparum
Abstract

BACKGROUND: DNA microarrays have been a valuable tool in malaria research for over a decade but remain in limited use in part due their relatively high cost, poor availability, and technical difficulty. With the aim of alleviating some of these factors next-generation DNA microarrays for genome-wide transcriptome analysis for both Plasmodium falciparum and Plasmodium berghei using the Agilent 8 x 15 K platform were designed.

METHODS: Probe design was adapted from previously published methods and based on the most current transcript predictions available at the time for P. falciparum or P. berghei. Array performance and transcriptome analysis was determined using dye-coupled, aminoallyl-labelled cDNA and streamlined methods for hybridization, washing, and array analysis were developed.

RESULTS: The new array design marks a notable improvement in the number of transcripts covered and average number of probes per transcript. Array performance was excellent across a wide range of transcript abundance, with low inter-array and inter-probe variability for relative abundance measurements and it recapitulated previously observed transcriptional patterns. Additionally, improvements in sensitivity permitted a 20-fold reduction in necessary starting RNA amounts, further reducing experimental costs and widening the range of application.

CONCLUSIONS: DNA microarrays utilizing the Agilent 8 x 15 K platform for genome-wide transcript analysis in P. falciparum and P. berghei mark an improvement in coverage and sensitivity, increased availability to the research community, and simplification of the experimental methods.

DOI10.1186/1475-2875-11-187
Alternate JournalMalar J
PubMed ID22681930
PubMed Central IDPMC3411454
Grant List1 DP2 OD 001315 / OD / NIH HHS / United States
DP2 OD001315 / OD / NIH HHS / United States
R01 AI076276 / AI / NIAID NIH HHS / United States
P50 GM0715078 / GM / NIGMS NIH HHS / United States
P50 GM071508 / GM / NIGMS NIH HHS / United States
/ / Howard Hughes Medical Institute / United States

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