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

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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.