High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing

Shin, D.; Urbanek, M. E.; Larson, H. H.; Moussa, A. J.; Lee, K. Y.; Baker, D. L.; Standen-Bloom, E.; Ramachandran, S.; Bogdanoff, D.; Cadwell, C. R.; Nowakowski, T. J.

doi:10.1101/2024.10.01.616167

bioRxiv · 10.1101/2024.10.01.616167

High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing

Shin, D.·Urbanek, M. E.·Larson, H. H.·Moussa, A. J.·Lee, K. Y.·Baker, D. L.·Standen-Bloom, E.·Ramachandran, S.·Bogdanoff, D.·Cadwell, C. R.·Nowakowski, T. J.

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Abstract

Single cell genomics has revolutionized our understanding of neuronal cell types. However, scalable technologies for probing single-cell connectivity are lacking, and we are just beginning to understand how molecularly defined cell types are organized into functional circuits. Here, we describe a protocol to generate high-complexity barcoded rabies virus (RV) for scalable circuit mapping from tens of thousands of individual starter cells in parallel. In addition, we introduce a strategy for targeting RV-encoded barcode transcripts to the nucleus so that they can be read out using single-nucleus RNA sequencing (snRNA-seq). We apply this tool in organotypic slice cultures of the developing human cerebral cortex, which reveals the emergence of cell type- specific circuit motifs in midgestation. By leveraging the power and throughput of single cell genomics for mapping synaptic connectivity, we chart a path forward for scalable circuit mapping of molecularly-defined cell types in healthy and disease states.

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Shin, D., Urbanek, M. E., Larson, H. H., Moussa, A. J., Lee, K. Y., Baker, D. L., Standen-Bloom, E., Ramachandran, S., Bogdanoff, D., Cadwell, C. R., Nowakowski, T. J.. 2024-10-02. High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing. https://doi.org/10.1101/2024.10.01.616167

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