ArticleeLife2024
Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing.
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 17 citations in OpenAlex.
- Mapping brain-wide monosynaptic inputs to single neurons with ROInet-seq.Cell reports methods · 2026Article
- An applicable and efficient retrograde monosynaptic circuit mapping tool for larval zebrafish.eLife · 2026Article
- Selective collateralization of transcriptomically distinct neurons organizes visual-stream output from the primary visual cortex.bioRxiv : the preprint server for biology · 2026Article
- Barcoded Rabies In Situ Connectomics for high-throughput reconstruction of neural circuits.Nature communications · 2026Article
- Protocol to produce and apply barcoded rabies virus for single-neuron input mapping in mice.STAR protocols · 2026Article
- Transsynaptic tracing techniques to interrogate neuronal connectivity of glioblastomas.Nature protocols · 2026Review
- A Tac1-Expressing Brainstem Pathway Underlies the Pathogenesis of Trigeminal Neuralgia.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Connectome-seq: high-throughput mapping of neuronal connectivity at single-synapse resolution via barcode sequencing.Nature methods · 2026Article
- Single-cell immune landscape of the central nervous system of mice infected with rabies virus.Frontiers in immunology · 2026Article
- Transsynaptic viral tools in neural circuit analysis: from anatomical mapping to functional interrogation.Frontiers in neural circuits · 2026Review
- Development and application of a barcoded rabies viral tracing method for mapping brain-wide inputs to single neurons.Cell reports methods · 2025Article
- One-step approach producing barcoded rabies virus with optimized diversity.Cell reports methods · 2025Article
- Dissecting mammalian cortical circuit development at single-cell resolution using inducible barcoded rabies virus.bioRxiv : the preprint server for biology · 2025Article
- Circuit-specific gene editing for precision modulation of neuronal activity with CRISPR-rabies virus.bioRxiv : the preprint server for biology · 2025Article
- Article
- Advances in Single-Cell Sequencing for Infectious Diseases: Progress and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing.bioRxiv : the preprint server for biology · 2025Article
- High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing.bioRxiv : the preprint server for biology · 2024Article
- Article
- Molecular connectomics reveals a glucagon-like peptide 1-sensitive neural circuit for satiety.Nature metabolism · 2024Article
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4130 retrogradely labeled cells and 2914 transsynaptically labeled cells in situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq and in situ sequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.