Advancing the Scientific Potential of Transcriptomics in Aquatic Models

提升水生模型转录组学的科学潜力

• 批准号: 8216288
• 负责人: WILLIAM A CRESKO
• 金额: $ 55.32万
• 依托单位: UNIVERSITY OF OREGON
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8216288
• 关键词: Age; Animal Model; Bioinformatics; Biological Models; Communities; Computer software; Computers; Costs and Benefits; DNA Sequence; Data; Data Analyses; Databases; Disease; Disease model; Educational workshop; Ensure; Expressed Sequence Tags; Fishes; Galaxy; Gene Expression; Gene Expression Process; Gene Expression Profile; Gene Expression Regulation; Generations; Genes; Genetic; Genetic Transcription; Genome; Genomics; Genotype; Goals; Health; Human; Internet; Intervention; Investigation; Knowledge; Laboratories; Lead; Length; Libraries; Maps; Medical; Methods; Modeling; Oceans; Online Systems; Oregon; Organ; Organism; Orthologous Gene; Outcome; Principal Investigator; Production; Protocols documentation; Reaction; Reading; Relative (related person); Research; Research Personnel; Resources; Role; Route; Running; Scientific Advances and Accomplishments; Scientist; Source; Speed; System; Technology; Time; Training; Transcript; Universities; Variant; Vertebrates; Voice; Work; aquatic organism; computer cluster; cost; graphical user interface; high throughput analysis; human disease; improved; insight; meetings; novel; parallel processing; research study; sex; theories; tool; transcriptomics

DESCRIPTION (provided by applicant): Human disease often involves changes in the timing and level of gene expression, processes investigated by transcriptomics, the identification of each expressed gene and its transcriptional levels. Studies of the association of human variation with altered gene expression can lead to a deeper, mechanistic understanding of disease states and can suggest therapies. A promising route to discovery is the transcriptomic analysis of novel models of common human diseases in aquatic species for which few genomic resources presently exist. Breakthroughs in sequencing technologies have opened the door for transcriptomics in non-model organisms. As detailed at the Sept. 2010 workshop 'Realizing the Scientific Potential of Transcriptomics in Aquatic Models', several impediments currently hinder the successful use of these tools in aquatic model systems. The goal of this project is to overcome these barriers by developing the protocols and tools necessary for researchers to capitalize on recent advances in DNA sequencing technology to better perform transcriptome analyses on aquatic medical models. This project will develop optimal laboratory protocols, analytical theory and computational software for transcriptome analyses of aquatic models of human disease and will help researchers plan and analyze experimental results. Protocols and tools will be made available via the Galaxy web platform as easy-to-use interfaces for computational software and web-based tutorials. Because many researchers working with aquatic non-model organisms lack access to the latest sequencing facilities and computational expertise for the analysis of high throughput transcriptomics, mechanisms will be developed for aquatic model organism researchers to use the Univ. of Oregon High Throughput Sequencing Facility. Similarly, many researchers lack access to computer clusters sufficiently powerful to execute the computational demands of modern transcriptomics, so this project will increase the availability of computational pipelines running at the Univ. of Oregon. This project will therefore provide widely needed tools, raise barriers to progress, and improve methods and technologies for transcriptome analysis in aquatic medical models, thus advancing our understanding of the role of gene regulation in health and disease. PUBLIC HEALTH RELEVANCE (provided by applicant): Studies of gene expression in aquatic model organisms promise significant breakthroughs in our understanding of the genetic causes of human diseases that can significantly increase human health. This project will accelerate research on non-model aquatic organisms by developing best practices and tools, making resources and training available, providing resources for laboratories to generate and analyze new types of genetic data and by contributing to the training of computer scientists in bioinformatics.

描述（由申请人提供）：人类疾病通常涉及基因表达的时间和水平的变化，转录组学研究的过程，每个表达基因及其转录水平的鉴定。研究人类变异与基因表达改变之间的关系，可以对疾病状态有更深入的机械理解，并可以提出治疗方法。一个有前途的发现途径是转录组学分析的新模式，常见的人类疾病的水生物种，目前存在的基因组资源很少。测序技术的突破为非模式生物的转录组学打开了大门。详细介绍了9 2010年研讨会“实现转录组学在水生模型中的科学潜力”，目前有几个障碍阻碍了这些工具在水生模型系统中的成功使用。该项目的目标是通过开发研究人员利用DNA测序技术最新进展所需的协议和工具来克服这些障碍，以更好地对水生医学模型进行转录组分析。该项目将为人类疾病水生模型的转录组分析开发最佳实验室方案、分析理论和计算软件，并将帮助研究人员规划和分析实验结果。将通过银河网络平台提供协议和工具，作为计算软件和网络教程的易用界面。由于许多研究水生非模式生物的研究人员无法获得最新的测序设施和计算专业知识，用于高通量转录组学分析，因此将为水生模式生物研究人员开发使用俄勒冈州大学高通量测序设施的机制。同样，许多研究人员缺乏足够强大的计算机集群来执行现代转录组学的计算需求，因此该项目将增加俄勒冈州大学运行的计算管道的可用性。因此，该项目将提供广泛需要的工具，提高进展的障碍，并改善水生医学模型中转录组分析的方法和技术，从而促进我们对基因调控在健康和疾病中的作用的理解。 公共卫生相关性（由申请人提供）：水生模式生物中基因表达的研究有望在我们对人类疾病遗传原因的理解方面取得重大突破，从而显著提高人类健康水平。该项目将通过开发最佳做法和工具、提供资源和培训、为实验室提供生成和分析新型遗传数据的资源以及促进对计算机科学家进行生物信息学培训，加速对非模式水生生物的研究。