Opening gene expression data to the research community

向研究界开放基因表达数据

• 批准号: BB/X018636/1
• 负责人: Craig Simpson
• 金额: $ 21.73万
• 依托单位: James Hutton Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FX018636%2F1
• 关键词: Opening; gene; expression; data; research

Gene expression and regulation is the foundation of plant development, organ specific differences and response to environment. RNA-Seq is a high-throughput sequencing technology that has become the primary platform for the study of gene and transcript level expression. Public data archives store vast volumes of raw RNA-Seq data that requires specialist analysis skills and large-scale computational resources to be of value to biologists and is thus an underutilised resource. Since our first attempt at accessing and processing quantitative gene expression data from publicly archived RNA-seq samples, the number of barley RNA-seq datasets have increased >5 fold, which brings challenges in the scale of processing and visualising large numbers of datasets. We propose to build on our existing barley gene expression database and website, EORNA, to provide a scalable, highly automated system for the discovery, retrieval and quantification of barley RNA-seq data. Comparative visualisation of transcript-level expression data will be coupled to improved curation of the experimental metadata. We will update and expand our current EORNA database with all available public barley RNA-Seq data, quantified against the latest state-of-the-art barley pan-transcriptome reference dataset. We will provide scalable transcript expression level plots with direct access to gene sequence information and annotation through an enhanced and easily searchable website. Finally, we will make the entire system generic and provide it as a free resource to the wider scientific community so that researchers working on other organisms can establish their own species-specific databases. Together, this will create an essential gene and gene transcript discovery resource for barley researchers and breeders, and the wider scientific community.

基因表达调控是植物发育、器官特异性差异和对环境响应的基础。RNA-Seq是一种高通量测序技术，已成为研究基因和转录水平表达的主要平台。公共数据档案存储了大量的原始RNA-Seq数据，这些数据需要专业分析技能和大规模计算资源才能对生物学家有价值，因此是一种未充分利用的资源。自从我们首次尝试访问和处理来自公开存档的RNA-seq样本的定量基因表达数据以来，大麦RNA-seq数据集的数量增加了5倍以上，这给处理和可视化大量数据集的规模带来了挑战。我们建议建立在我们现有的大麦基因表达数据库和网站EORNA上，为大麦RNA-seq数据的发现，检索和定量提供一个可扩展的，高度自动化的系统。转录水平表达数据的比较可视化将与实验元数据的改进管理相结合。我们将更新和扩展我们目前的EORNA数据库，其中包含所有可用的公共大麦RNA-Seq数据，这些数据是根据最新的最先进的大麦泛转录组参考数据集进行量化的。我们将提供可扩展的转录表达水平图，通过增强和易于搜索的网站直接访问基因序列信息和注释。最后，我们将使整个系统通用，并将其作为免费资源提供给更广泛的科学界，以便研究其他生物的研究人员可以建立自己的物种特异性数据库。总之，这将为大麦研究人员和育种者以及更广泛的科学界创造一个重要的基因和基因转录本发现资源。