Development of nonhuman primate reference transcriptome resources

描述（由申请人提供）：我们建议使用lllumina的下一代测序平台生成全面的非人灵长类动物（NHP）参考转录组数据库。这些数据库将包含蛋白质编码、长非编码和小非编码转录本的信息，并将提供大量关于基因和转录本结构、表达和调控的新信息。为了增强这一资源，我们还将生成恒河猴组织特异性转录组图谱和NHP艾滋病模型的全转录组信息。这些数据库将为从事进化、比较生物学、遗传学、基因组学和人类疾病NHP模型研究的科学家提供资源。在Aim 1中，我们将与lllumina科学家合作，生成14个NHP物种/亚种的全转录组（蛋白质编码和长非编码）信息，lllumina将对应用程序进行免费测序。这些NHP基因组中的大部分将在年内测序，转录组信息将促进基因组组装、注释，为系统生物学研究开发新工具，同时也为进化生物学家提供广泛的资源。为了补充整个转录组项目，我们将使用我们的lllumina基因组分析仪生成恒河猴的组织特异性转录组，恒河猴是生物医学研究中使用最广泛的NHP。在Aim 2中，我们将对来自一项独立资助的研究的蛋白质编码、长非编码和小非编码转录本进行测序，该研究专注于艾滋病的NHP急性感染模型。由此产生的数据将扩展NHP参考转录组数据库，包括有关病毒-宿主相互作用、先天免疫、炎症过程、向适应性免疫反应的过渡以及感染诱导转录本的新信息。最后，来自两个Aims的全转录组数据将使非编码rna的发现和量化成为可能，这些非编码rna具有广泛的功能，但尚未得到很好的理解。鉴于NHP灵长类动物作为人类健康和疾病模型的重要性，获得这些动物的完整转录组信息是当务之急。

DESCRIPTION (provided by applicant): We propose to generate comprehensive nonhuman primate (NHP) reference transcriptome databases using lllumina's next-generation sequencing platform. These databases will contain information on protein-coding, long noncoding, and small noncoding transcripts, and will provide vast amounts of new information regarding gene and transcript structure, expression, and regulation. To enhance this resource, we will also generate a tissue-specific transcriptome atlas for rhesus macaque and whole transcriptome information from a NHP model of AIDS. These databases will serve as a resource for scientists working on evolution, comparative biology, genetics, genomics, and NHP models of human disease. In Aim 1, we will collaborate with lllumina scientists to generate whole transcriptome (protein-coding and long noncoding) information for 14 NHP species/subspecies, lllumina will perform this sequencing at no cost to the application. The majority of these NHP genomes will be sequenced within the year, and transcriptome information will facilitate genome assembly, annotation, development of new tools for systems biology research, while also providing broad resources for evolutionary biologists. To complement the whole transcriptome project, we will use our lllumina Genome Analyzer to generate a tissue specific transcriptome for rhesus macaque, the most widely used NHP in biomedical research. In Aim 2, we will sequence protein-coding, long noncoding, and small noncoding transcripts from an independently funded study focused on a NHP acute infection model of AIDS. The resulting data will expand the NHP reference transcriptome databases to include new information on virus-host interactions, innate immunity, inflammatory processes, the transition to the adaptive immune response, and infection-induced transcripts. Finally, whole transcriptome data from both Aims will enable the discovery and quantification of noncoding RNAs, which have widespread functionality but are not well understood. Given the importance of NHP primates as models for human health and disease, it is imperative that whole transcriptome information be available for these animals.