Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
Malar J. 2012 Jun 8;11:187. doi: 10.1186/1475-2875-11-187.
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.
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.
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.
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.
DNA 微阵列在疟疾研究中已经是一个有价值的工具超过十年了，但仍然由于其相对较高的成本、较差的可用性和技术难度，使用范围有限。为了缓解其中的一些因素，我们设计了新一代的 DNA 微阵列，用于 Plasmodium falciparum 和 Plasmodium berghei 的全基因组转录组分析，使用的是 Agilent 8 x 15 K 平台。
探针设计是从以前发表的方法改编而来的，并且基于当时 Plasmodium falciparum 或 Plasmodium berghei 最新的转录本预测。使用染料偶联的、氨基丙炔基标记的 cDNA 以及杂交、洗涤和阵列分析的简化方法来确定阵列性能和转录组分析。
新的阵列设计在涵盖的转录本数量和每个转录本的平均探针数量方面都有显著的改进。阵列性能在广泛的转录本丰度范围内都非常出色，具有低的阵列间和探针间的相对丰度测量的可变性，并且它再现了先前观察到的转录模式。此外，灵敏度的提高使得所需起始 RNA 量减少了 20 倍，进一步降低了实验成本，扩大了应用范围。
利用 Agilent 8 x 15 K 平台进行 Plasmodium falciparum 和 Plasmodium berghei 全基因组转录分析的 DNA 微阵列在覆盖范围和灵敏度方面都有了提高，增加了研究社区的可用性，并简化了实验方法。
