Development of nonhuman primate reference transcriptome resources

非人灵长类参考转录组资源的开发

• 批准号: 8494707
• 负责人: MICHAEL G KATZE
• 金额: $ 73.16万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8494707
• 关键词: AIDS Vaccines; Acquired Immunodeficiency Syndrome; Acute; Amino Acid Sequence; Animals; Archives; Atlases; Binding Sites; Bioinformatics; Biology; Biomedical Research; Charge; Code; Communities; Comparative Biology; Complement; Data; Data Analyses; Data Set; Databases; Deposition; Development; Developmental Process; Disease; Drug Targeting; Evolution; Exons; Funding; Gene Expression; Gene Expression Profile; Gene Proteins; Genes; Genetic; Genetic Transcription; Genome; Genomics; Goals; Health; Human; Immune response; Infection; Inflammatory; Introns; Investigation; Letters; Light; Macaca; Macaca mulatta; MicroRNAs; Modeling; Monoclonal Antibody R24; National Center for Research Resources; Natural Immunity; Peptide Sequence Determination; Phase; Primates; Principal Investigator; Process; Proteins; Proteomics; RNA; RNA Sequence Analysis; Reading; Regulation; Research; Research Activity; Research Personnel; Resource Development; Resources; Role; SIV; Sampling; Scientist; Staging; Structure; Systems Biology; Technology; Tissue Sample; Tissues; Transcript; Translational Research; Untranslated RNA; Vaccine Research; Variant; Virus Diseases; Work; computerized data processing; cost; design; genome sequencing; human disease; next generation sequencing; nonhuman primate; novel vaccines; programs; research study; response; tool; tool development; virus host interaction; web site; working group

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.

描述（由申请人提供）：我们提出使用Illumina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。这些数据库将包含有关蛋白质编码、长非编码和小非编码转录本的信息，并将提供有关基因和转录本结构、表达和调控的大量新信息。为了增强这一资源，我们还将生成恒河猴的组织特异性转录组图谱和来自艾滋病NHP模型的全转录组信息。这些数据库将作为研究进化、比较生物学、遗传学、基因组学和人类疾病NHP模型的科学家的资源。在Aim 1中，我们将与Illumina科学家合作，为14个NHP物种/亚种生成全转录组（蛋白质编码和长非编码）信息，Illumina将免费进行此测序。这些NHP基因组中的大多数将在年内测序，转录组信息将促进基因组组装，注释，开发系统生物学研究的新工具，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Illumina基因组分析仪为恒河猴生成组织特异性转录组，这是生物医学研究中使用最广泛的NHP。在目标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，该研究的重点是艾滋病的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，以包括有关病毒-宿主相互作用，先天免疫，炎症过程，向适应性免疫反应过渡以及感染诱导转录的新信息。最后，来自两个目标的全转录组数据将使非编码RNA的发现和定量成为可能，这些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，必须为这些动物提供完整的转录组信息。