A high-resolution molecular and lineage atlas of the mouse brain using Slide-seq

项目摘要 小鼠大脑由数千种高度特化的细胞类型组成，分布在数百个细胞中。 解剖区域最近，DNA条形码和测序的进展使大规模调查成为可能。 转录状态（单细胞RNA序列）和表观遗传状态（单细胞DNA甲基化和ATACseq） 穿过大脑随着细胞类型库存开始在未来1-2年内变得可用， 出现了：高通量技术，可以将这些分子数据与细胞类型的其他特征联系起来 身份，包括血统，连接，组织学和功能活动。在这里，我们建议部署两个 我们在实验室开发的技术-Slide-seq，一种测量基因组全表达的技术， 10微米分辨率的组织切片，以及TRACE，一种用于连续遗传记录的新方法， 哺乳动物系统中的多样化-系统地绘制脑中所有转录定义的细胞类型， 并将这些细胞类型与特定的神经发育谱系联系起来。首先，我们将在132上执行Slide-seq 冠状切片从一个单一的一半的大脑，提供了一个全面的看法基因表达在原位。 其次，我们将使用条形码慢病毒和TRACE的组合在全脑范围内重建细胞谱系， 通过我们将作为这个项目的一部分产生的转基因菌株来传递。总之，这项工作将提供 最全面的小鼠大脑空间和发育特征，作为一个基础 数据集，以了解哺乳动物神经系统的结构和功能。

PROJECT SUMMARY The mouse brain is composed of thousands of highly specialized cell types, distributed across hundreds of anatomical regions. Recently, advances in DNA barcoding and sequencing have enabled large-scale surveys of transcriptional state (single cell RNAseq), and epigenetic state (single cell DNA methylation and ATACseq) across the brain. As cell type inventories begin becoming available in the coming 1-2 years, a crucial need has emerged: high throughput technologies that can connect these molecular data to other features of cell type identity, including lineage, connectivity, histology, and functional activity. Here, we propose to deploy two technologies we developed in our labs—Slide-seq, a technology that measures genome-wide expression in tissue sections at 10 micron resolution, and TRACE, a novel method for continuous genetic recording and diversification in mammalian systems—to systematically map all transcriptionally defined cell types in the brain, and to relate these cell types to specific neurodevelopmental lineages. First, we will perform Slide-seq on 132 coronal sections from a single half of the brain, providing a comprehensive view of gene expression in situ. Second, we will reconstruct cell lineage brain-wide using a combination of barcoded lentiviruses, and TRACE, delivered through a transgenic strain we will generate as part of this project. Together, this work will provide the most comprehensive spatial and developmental characterization of the mouse brain, serving as a foundational dataset for understanding the structure and function of the mammalian nervous system.