疟原虫属的全基因组分析。利用新型安捷伦科技DNA微阵列平台。

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

作者信息

Painter Heather J, Altenhofen Lindsey M, Kafsack Björn F C, Llinás Manuel

机构信息

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

出版信息

Methods Mol Biol. 2013;923:213-9. doi: 10.1007/978-1-62703-026-7_14.

DOI:10.1007/978-1-62703-026-7_14

PMID:22990780

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.

摘要

DNA微阵列技术在疟疾基因组学中的应用已被广泛使用，但受到样本可用性和技术变异性的限制。为了解决这些问题，我们提出了一种微阵列杂交方案，该方案已针对两种用于恶性疟原虫和伯氏疟原虫的新型安捷伦科技DNA微阵列进行了优化。利用每个物种的最新可用基因组序列，我们为每个物种设计了约14,000个寡核苷酸探针，代表约5,600个转录本。每个阵列设计中都包含许多探针，可用于识别寄生虫发育阶段、基因操作中常用的疟原虫分子标记以及用于控制阵列一致性和质量的制造商探针。总体而言，安捷伦疟原虫属阵列设计和杂交方法为其他目前可用的微阵列平台提供了一种灵敏、易用、高质量且经济高效的替代方案。