New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community
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 gen...
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ftdoajarticles:oai:doaj.org/article:20e72adda3854cd8b4153ba113e04d1f 2023-05-15T15:10:03+02:00 New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community Kafsack Björn F C Painter Heather J Llinás Manuel 2012-06-01T00:00:00Z https://doi.org/10.1186/1475-2875-11-187 https://doaj.org/article/20e72adda3854cd8b4153ba113e04d1f EN eng BMC http://www.malariajournal.com/content/11/1/187 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-11-187 1475-2875 https://doaj.org/article/20e72adda3854cd8b4153ba113e04d1f Malaria Journal, Vol 11, Iss 1, p 187 (2012) Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2012 ftdoajarticles https://doi.org/10.1186/1475-2875-11-187 2022-12-31T13:51:02Z 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 8x15K 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 8x15K 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 11 1 187 |
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Directory of Open Access Journals: DOAJ Articles |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Kafsack Björn F C Painter Heather J Llinás Manuel New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community |
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Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
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 8x15K 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 8x15K 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. |
format |
Article in Journal/Newspaper |
author |
Kafsack Björn F C Painter Heather J Llinás Manuel |
author_facet |
Kafsack Björn F C Painter Heather J Llinás Manuel |
author_sort |
Kafsack Björn F C |
title |
New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community |
title_short |
New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community |
title_full |
New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community |
title_fullStr |
New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community |
title_full_unstemmed |
New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community |
title_sort |
new agilent platform dna microarrays for transcriptome analysis of plasmodium falciparum and plasmodium berghei for the malaria research community |
publisher |
BMC |
publishDate |
2012 |
url |
https://doi.org/10.1186/1475-2875-11-187 https://doaj.org/article/20e72adda3854cd8b4153ba113e04d1f |
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Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 11, Iss 1, p 187 (2012) |
op_relation |
http://www.malariajournal.com/content/11/1/187 https://doaj.org/toc/1475-2875 doi:10.1186/1475-2875-11-187 1475-2875 https://doaj.org/article/20e72adda3854cd8b4153ba113e04d1f |
op_doi |
https://doi.org/10.1186/1475-2875-11-187 |
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Malaria Journal |
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11 |
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1 |
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187 |
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1766341117145513984 |