Protocol for mapping neural circuit connectivity with START: Single transcriptome assisted rabies tracing.

Maribel Patiño, Sai Krishna Bhamidipati, Christian Cazares, Edward M Callaway

Abstract read

In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

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0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Maribel PatiñoSystems Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA. Electronic address: m3patino@health.ucsd.edu.

Sai Krishna BhamidipatiSystems Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.

Christian CazaresSystems Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA.

Edward M CallawaySystems Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA. Electronic address: callaway@salk.edu.

Funding

Investigating Orbitofrontal Circuit Mechanisms of Social Rank and Dominance BehaviorK00MH132569 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CAZARES, CHRISTIAN · 2022 to 2025

$318k

NIMH NIH HHS K00 MH132569

6 · The paper itself

Abstract

Characterizing neural connectivity at transcriptomic cell-type resolution is essential for understanding neural mechanisms of circuit function. Here, we present single transcriptome assisted rabies tracing (START), a protocol combining monosynaptic rabies tracing with single-nucleus RNA sequencing to identify transcriptomic cell types providing inputs to defined neuronal populations in the mouse cortex. We describe steps for Cre-dependent helper virus injection, EnvA-pseudotyped rabies infection, tissue microdissection, and fluorescence-activated nuclei sorting. We then detail procedures for library preparation and computational annotation of nuclei. For complete details on the use and execution of this protocol, please refer to Patiño et al.

Indexed as

RabiesRabies virusTranscriptomeAnimalsMiceNeuronsmodel OrganismsMolecular BiologyNeuroscienceRNAseq

Identifiers

PMID42284148

DOI10.1016/j.xpro.2026.104634

PMCPMC13309977

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LicenceCC BY

Read underepoch 390

Registered trials

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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.