Protocol to produce and apply barcoded rabies virus for single-neuron input mapping in mice.

Overview

1. Lingang Laboratory, Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, 555 Qiangye Road, Shanghai 201210, China

Abstract

Barcoded rabies viral tracing enables high-throughput mapping of brain-wide inputs to individual neurons while allowing integration with transcriptomic profiling. Here, we present a protocol to produce and apply barcoded rabies virus in mice for single-neuron input mapping. We describe steps to generate barcode plasmid libraries, produce barcoded rabies virus, and isolate target brain regions. We then detail procedures for preparing single-cell suspensions or bulk RNA, building barcode amplicon libraries from input regions, and performing initial analysis of the sequencing data.

For complete details on the use and execution of this protocol, please refer to Tan et al.1,2

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

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The paper's code and data availability statement is in the Data section.

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Data

Datasets cited

• figshare:31072744, at figshare; found in “Data and code availability”

Data and code availability

Original data have been deposited to Figshare: https://doi.org/10.6084/m9.figshare.31072744. The code used to analyze the data is also publicly available at the same Figshare repository.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 7 keywords, 7 MeSH terms, 1 funder, 7 references.

Cite

This paper

Tan, K., Wang, Y.-q., Fan, L., & Xu, H.-t. (2026). Protocol to produce and apply barcoded rabies virus for single-neuron input mapping in mice. STAR protocols, 7(2), 104537. https://doi.org/10.1016/j.xpro.2026.104537

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