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

使用 Slide-seq 绘制小鼠大脑的高分辨率分子和谱系图谱

基本信息

批准号：
10088261
负责人：
Fei Chen
金额：
$ 190.31万
依托单位：
BROAD INSTITUTE, INC.
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-18 至 2023-09-17
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10088261
关键词：
ATAC-seq Adult Anatomy Animal Model Atlases Bacteriophages Bar Codes Behavior Biological Assay Brain Cell Lineage Cell Nucleus Cells Complex Coupled Cytidine Deaminase DNA DNA Methylation Data Data Set Development Epigenetic Process Equipment Equipment and supply inventories Female Foundations Gene Expression Genetic Genetic Transcription Histology In Situ Individual Institutes Interneurons Libraries Location Maps Measurement Measures Methods Molecular Mus Nervous system structure Neurobiology Polymerase Population Population Heterogeneity Positioning Attribute RNA Resolution Sampling Site Slide Small Nuclear RNA Structure Subfamily lentivirinae Surveys System Technology Tissues Transgenic Organisms Trees Work base brain volume cell type density genome-wide high throughput technology in vivo male new technology novel oligo (dT)reconstruction single cell sequencing single-cell RNA sequencing synthetic biology tool transcriptome sequencing transcriptomics

项目摘要

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.

项目概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。最近，DNA 条形码和测序技术的进步使得大规模调查成为可能。转录状态（单细胞 RNAseq）和表观遗传状态（单细胞 DNA 甲基化和 ATACseq）随着细胞类型库存在未来 1-2 年内开始可用，出现了至关重要的需求。出现了：可以将这些分子数据与细胞类型的其他特征连接起来的高通量技术身份，包括谱系、连接性、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，一种测量基因组范围表达的技术 10 微米分辨率的组织切片，以及 TRACE（一种连续基因记录和分析的新方法）哺乳动物系统的多样化——系统地绘制大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，我们将对 132 进行 Slide-seq。来自大脑半部的冠状切片，提供原位基因表达的全面视图。其次，我们将使用条形码慢病毒和 TRACE 的组合来重建全脑细胞谱系，作为该项目的一部分，我们将通过转基因菌株来交付，这项工作将共同提供。最全面的小鼠大脑空间和发育特征，作为基础用于了解哺乳动物神经系统的结构和功能的数据集。