{"doi":"10.1101/2024.10.01.616167","title":"High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing","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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":484748,"datarank":0.32958368660043297,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.0,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":8,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9502,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1326918,"name":"M Urbanek","orcid":"0000-0002-0320-2260","position":1,"is_corresponding":false},{"id":1208215,"name":"H. Hanh Larson","orcid":null,"position":2,"is_corresponding":false},{"id":983491,"name":"Anthony Moussa","orcid":"0000-0002-9538-2747","position":3,"is_corresponding":false},{"id":1326919,"name":"Kevin Y. Lee","orcid":"0000-0002-1528-7417","position":4,"is_corresponding":false},{"id":1326920,"name":"Donovan L Baker","orcid":"0009-0008-6928-3252","position":5,"is_corresponding":false},{"id":1327389,"name":"Elio Standen-Bloom","orcid":null,"position":6,"is_corresponding":false},{"id":1171974,"name":"Sangeetha Ramachandran","orcid":"0009-0002-9674-3310","position":7,"is_corresponding":false},{"id":476077,"name":"Derek Bogdanoff","orcid":null,"position":8,"is_corresponding":false},{"id":59109,"name":"Cathryn R. Cadwell","orcid":"0000-0003-1963-8285","position":9,"is_corresponding":false},{"id":21360,"name":"Tomasz J. Nowakowski","orcid":"0000-0003-2345-4964","position":10,"is_corresponding":false},{"id":307691,"name":"David Shin","orcid":"0000-0001-7029-089X","position":0,"is_corresponding":true}],"reference_count":103,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:07:42.971417Z","pmid":"39713304","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}