NSF EAGER: A cross-kingdom comparison of single cell transcriptomes

细胞是所有活着的有机体的基石，有机体内不同的细胞类型是由它们表达的哪些基因来定义的。然而，定义特定细胞类型的确切基因表达谱在很大程度上是未知的。此外，还不知道细胞如何表达定义一种细胞类型与另一种细胞类型的一组基因，也不知道指定细胞类型的规则是否在植物和动物之间有所不同。最后一个问题特别有趣，因为在这两个不同的王国中，多细胞是独立进化的。该项目将通过测序和分析不同类型的单个玉米细胞的mRNA来解决这些重要问题，使这些序列及其方法和分析程序可供更广泛的植物研究社区使用。该项目还将通过培训本科生和高中生进行基因组学和计算生物学方面的推广和教育，作为冷泉港实验室本科研究计划和CSHL未来伙伴计划的一部分，冷泉港实验室本科研究计划的重点是数量生物学，这两个计划都是培训科学界代表性不足的群体的成员。来自这些项目的学生将在湿实验室实验以及生物信息学和验证实验中参与这一项目，提供发育生物学和计算生物学的跨学科培训。生物体的发育和功能是通过不同专门化细胞类型之间的复杂相互作用来实现的。使用一种优化的方案对正在发育的玉米花序进行原生质体培养，这个团队将从这个发育器官的不同区域快速分离出数十万个单细胞。该项目将应用细胞生物学、基因组学和单细胞基因表达分析方面的专业知识来识别玉米中的细胞特异性表达特征，并询问植物和动物之间细胞类型规格的比较。一项变革性的新技术，单细胞RNA测序(scRNA-seq)，首次提供了描述单个植物细胞并在一个全新的水平上了解植物发育的机会。这种方法有能力理解细胞类型特定的网络，理解细胞类型内转录的异质性，并识别细胞命运的新调节因子。该项目将测试不同的scRNA-seq技术，并开发可被植物界广泛采用的信息学工具，并将对不同生命王国的单细胞转录给予独特的见解。因此，这个项目有可能揭示在整个王国范围内指定细胞类型的规则。该项目中产生的数据将开放用于重新分析和与其他数据集整合。该项目还将开发和调整将广泛适用于植物社区的单细胞分析方法。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Cells are the building blocks of all living organisms and different cell types within an organism are defined by which of their genes they express. However, the precise gene expression profiles that define specific cell types are largely unknown. In addition, it is not known how cells come to express the set of genes that define one cell type versus another or whether the rules that specify cell types differ between plants and animals. This last question is especially interesting because being multicellular evolved independently in these two different kingdoms. The project will address these important questions by sequencing and analyzing mRNA from individual maize cells of different types, making these sequences and their methods and analytical procedures available to the wider plant research community. The project will also contribute to outreach and education by training undergraduate and high school students in genomics and computational biology as part of the Cold Spring Harbor Laboratory Undergraduate Research Program, which has a focus in quantitative biology, as well as the CSHL Partners For The Future Program, both of which train members of groups underrepresented in science. Students from each of these programs will be engaged in this project in both wet lab experiments and in bioinformatics and validation experiments, providing cross-disciplinary training in developmental biology and computational biology. Living organisms develop and function by complex interactions between different specialized cell types. Using an optimized protocol to protoplast developing maize inflorescences, this team will isolate hundreds of thousands of single cells rapidly from different regions of this developing organ. The project will apply expertise in cell biology, genomics and single cell gene expression analysis to identify cell specific expression signatures in maize and to ask how cell type specification compares between plants and animals. A transformative new technology, single cell RNA sequencing (scRNA-seq), offers for the first time the opportunity to profile single plant cells and understand plant development at a fundamentally new level. This method has the power to understand cell type specific networks, to understand transcriptional heterogeneity within cell types and to identify novel regulators of cell fate. The project will test different scRNA-seq technologies and develop informatics tools that can be widely adopted by the plant community, and will be transformative in giving unique insights into single cell transcriptomes across different kingdoms of life. Therefore, this project has the potential to uncover the rules by which cell types are specified across kingdom wide scales. Data generated in this project will be openly available for reanalysis and integration with other datasets. The project will also develop and adapt single cell analysis methods that will be broadly applicable for the plant community.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.