FlyAtlas2: a definitive, expanded NGS expression resource for the Drosophila community and beyond

FlyAtlas2：果蝇社区及其他领域的权威、扩展的 NGS 表达资源

• 批准号: BB/K019953/1
• 负责人: Julian Dow
• 金额: $ 77.2万
• 依托单位: University of Glasgow
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK019953%2F1
• 关键词: FlyAtlas2; definitive; expanded; NGS; expression

Now that many genomes (of humans and other organisms) have been sequenced, we know that most animals are made with about 15 000 - 25 000 genes. Perhaps surprisingly, we still do not know what all these genes do, and we are still discovering entirely new genes. A vital tool to understanding what genes do is simply to see where the genes are being used (or "expressed"). Then we can mutate the genes in a simple model organism, and see what changes in those tissues - this is called 'reverse genetics', and is a key part of post-genomic research. The simple fruit fly Drosophila is an excellent model for such studies, because of its uniquely powerful genetics, and is used by many thousands of labs around the world. As well as being an important organism to study in its own right, it has proved a valuable model both for human function and disease, and for study of closely related insect pests and vectors of disease.In 2007, we produced FlyAtlas.org, an online atlas of gene expression across multiple tissues (brain, heart, gut, muscle etc) of both larval and adult flies, using the then cutting-edge technology of Affymetrix microarrays. With this resource, users could quickly (in typically 10 seconds) get an answer to the question "where and when in the organism is my gene of interest expressed?" As FlyAtlas saves the need to go off and do a series of expensive experiments, this website thus saves many days of work each time it is used. This database revealed a great hunger for such data, both in the Drosophila research community and beyond, and the data have already been used in over 650 papers from around the world. However, since then the technology has rapidly advanced, and 'next generation sequencing (NGS)' allows us to provide a much more complete picture. In particular, we are not constrained by the genes printed on the Affymetrix chips, and can identify and measure the abundance of different transcripts from any gene. In addition, we will be able to identify novel variants of known transcripts, or even entirely new genes. We will also be able to map out the expression of tiny, 'micro RNAs' across multiple tissues. The result will be a step-change in how we are able to perform post-genomic research.All these data will be placed rapidly online -in the public domain- to inform and accelerate research worldwide. We will also work to evanglise the new, extended FlyAtlas resource both to the Drosophila community and beyond. As well as obvious benefits to scientists, the data will enable biomedical research using Drosophila, as many researchers are now successfully modelling human diseases in flies. Additionally, the work will benefit industry, as the data will help to inform the search for new classes of safer, 'greener' insecticides. This is important, because insects are major vectors of disease, and pests of crops, around the world.

既然许多基因组（人类和其他生物）已经测序，我们知道大多数动物是由大约15000 - 25000个基因组成的。也许令人惊讶的是，我们仍然不知道所有这些基因的作用，我们仍然在发现全新的基因。了解基因作用的一个重要工具就是看看基因在哪里被使用（或“表达”）。然后，我们可以在一个简单的模式生物中突变基因，看看这些组织发生了什么变化——这被称为“反向遗传学”，是后基因组研究的关键部分。简单的果蝇是这类研究的绝佳模型，因为它具有独特的强大基因，被世界上成千上万的实验室所使用。它不仅是一种值得研究的重要生物，而且已被证明是研究人体功能和疾病以及研究密切相关的害虫和疾病媒介的有价值的模型。2007年，我们利用当时最先进的Affymetrix微阵列技术，制作了FlyAtlas.org网站，这是一个关于幼虫和成年果蝇多个组织（大脑、心脏、肠道、肌肉等）基因表达的在线图谱。有了这个资源，用户可以很快（通常在10秒内）得到“我感兴趣的基因在生物体的什么地方和什么时候表达？”这个问题的答案。由于FlyAtlas节省了去做一系列昂贵的实验的需要，因此这个网站每次使用时都节省了许多天的工作。这个数据库揭示了对这类数据的巨大需求，无论是在果蝇研究界还是其他领域，这些数据已经被用于来自世界各地的650多篇论文中。然而，从那时起，这项技术迅速发展，“下一代测序（NGS）”使我们能够提供更完整的图像。特别是，我们不受Affymetrix芯片上打印的基因的限制，可以识别和测量来自任何基因的不同转录本的丰度。此外，我们将能够识别已知转录本的新变体，甚至是全新的基因。我们还将能够绘制出微小的“微rna”在多个组织中的表达。结果将是我们如何能够进行后基因组研究的一个步骤变化。所有这些数据将被迅速放到网上——在公共领域——为全世界的研究提供信息和加速。我们还将努力将新的、扩展的FlyAtlas资源传播给果蝇社区和其他社区。除了给科学家带来明显的好处外，这些数据还将使利用果蝇进行生物医学研究成为可能，因为许多研究人员现在已经成功地在果蝇身上建立了人类疾病的模型。此外，这项工作将使工业受益，因为这些数据将有助于为寻找更安全、更“环保”的新型杀虫剂提供信息。这一点很重要，因为昆虫是世界各地农作物疾病和害虫的主要传播媒介。

项目成果

Updates on ion and water transport by the Malpighian tubule.

• DOI: 10.1016/j.cois.2021.02.018
• 发表时间: 2021-10
• 期刊: Current opinion in insect science
• 影响因子: 5.3

Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia.

• DOI: 10.1186/1471-2164-14-518
• 发表时间: 2013-07-30
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Chintapalli VR;Wang J;Herzyk P;Davies SA;Dow JA
• 通讯作者: Dow JA

FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data.

• DOI: 10.1093/nar/gkx976
• 发表时间: 2018-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Leader DP;Krause SA;Pandit A;Davies SA;Dow JAT
• 通讯作者: Dow JAT

A nutrient-responsive hormonal circuit mediates an inter-tissue program regulating metabolic homeostasis in adult Drosophila.

• DOI: 10.1038/s41467-021-25445-2
• 发表时间: 2021-08-30
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Koyama T;Terhzaz S;Naseem MT;Nagy S;Rewitz K;Dow JAT;Davies SA;Halberg KV
• 通讯作者: Halberg KV

What is an epitheliome, anyway?

到底什么是上皮组？

• DOI: 10.1016/j.ibmb.2015.10.013
• 发表时间: 2015
• 期刊: Insect biochemistry and molecular biology
• 影响因子: 3.8
• 作者: Dow JA