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

细胞是所有生物体的基石，生物体内的不同细胞类型由它们表达的基因来定义。然而，定义特定细胞类型的精确基因表达谱在很大程度上是未知的。此外，目前还不知道细胞是如何表达一组定义一种细胞类型与另一种细胞类型的基因的，也不知道植物和动物之间指定细胞类型的规则是否不同。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界使用。 该项目还将通过培训本科生和高中生的基因组学和计算生物学作为冷泉港实验室本科生研究计划的一部分来促进推广和教育，该计划侧重于定量生物学，以及CSHL未来计划的合作伙伴，这两个计划都培训了科学中代表性不足的团体的成员。来自每个项目的学生将参与该项目的湿实验室实验和生物信息学和验证实验，提供发育生物学和计算生物学的跨学科培训。生物体通过不同特化细胞类型之间的复杂相互作用来发育和发挥功能。利用一种优化的方案来开发玉米花序的原生质体，该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，识别玉米中的细胞特异性表达特征，并研究植物和动物之间的细胞类型规格比较。一项变革性的新技术，单细胞RNA测序（scRNA-seq），首次提供了在一个全新的水平上分析单个植物细胞和了解植物发育的机会。这种方法有能力了解细胞类型特异性网络，了解细胞类型内的转录异质性，并确定新的调节细胞命运。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，并将在不同生命王国的单细胞转录组中提供独特的见解。因此，该项目有可能揭示在整个王国范围内指定细胞类型的规则。该项目生成的数据将公开提供，用于重新分析和与其他数据集集成。该项目还将开发和调整单细胞分析方法，将广泛适用于工厂社区。该奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

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.