OSCR

Control of innate olfactory valence by segregated cortical amygdala circuits.

Overview

Authors: James R Howe1,2,3, Chung Lung Chan1, Donghyung Lee1, Marlon Blanquart1, James H Lee1, Laurine Decoster1, Haylie K Romero2,3,4, Abigail N Zadina5, Mackenzie E Lemieux6, Fergil Mills6, Paula A Desplats3,4,7, Kay M Tye1,6,8, Cory M Root1
  1. Department of Neurobiology, University of California, San Diego La Jolla United States
  2. Neurosciences Graduate Program, University of California, San Diego La Jolla United States
  3. Department of Neurosciences, University of California, San Diego La Jolla United States
  4. Center for Circadian Biology, University of California, San Diego La Jolla United States
  5. Zuckerman Mind Brain Behavior Institute, Columbia University New York United States
  6. Salk Institute for Biological Sciences La Jolla United States
  7. Department of Pathology, University of California, San Diego La Jolla United States
  8. Howard Hughes Medical Institute La Jolla United States
Institutions: University of California San Diego (United States); Columbia University (United States); Salk Institute for Biological Studies (United States); Howard Hughes Medical Institute (United States)
Journal: eLife, volume 14, article RP104677
Dates: published online 23 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.7554/elife.104677 · PMID 41870253 · PMCID PMC13008359 · OpenAlex W4406213577
Open access: gold, a free copy (OpenAlex)
Status: code verified (how the code is found and verified)
Categories: mouse (organism), systems (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, Evoked potentials, Connectivity, fMRI & imaging, Single-unit activity, calcium imaging
Keywords: odor, innate behavior, cortical amygdala, valence, topographic organization, Mouse
MeSH: Amygdala*, Olfactory Pathways*, Olfactory Perception*, Smell*, Animals, Male, Mice, Mice, Inbred C57BL, Neurons, Odorants, Optogenetics (* major topic)
Journal subjects: Neuroscience
Topic: Olfactory and Sensory Function Studies (Sensory Systems, Neuroscience), according to OpenAlex
Funding: National Institute on Deafness and Other Communication Disorders (R01DC018313-01A1, R00DC014516-05); National Institute of Mental Health (R01MH115920-03, R37MH102441, K99MH121563-02); National Institute of Diabetes and Digestive and Kidney Diseases (DP2DK102256-01S1); National Center for Complementary and Integrative Health (DP1AT009925-04); National Institutes of Health (RF1AG061831-01S1); National Defense Science and Engineering Fellowship; Canadian Institutes of Health Research; Dolby Family Fund; Hellman Fellowship
Citations: cited by 8 papers (Europe PMC); 92 references in the paper
Research resources: AAVretro-hSyn-EGFP-Cre RRID:Addgene_105540, AAV9-hSyn-jGCaMP8s-WPRE RRID:Addgene_162374, AAV2-hSyn-DIO-hM4D(Gi)-mCherry RRID:Addgene_44362, AAV5-EF1A-mCherry-IRES-Cre-WPRE RRID:Addgene_55632, RRID:IMSR_JAX:000664, Arc-CreERT2 RRID:IMSR_JAX:022357, VGlut1-cre RRID:IMSR_JAX:023527, VGlut2-cre RRID:IMSR_JAX:028863, APP23 RRID:IMSR_JAX:030504, AAV5-hSyn-eYFP RRID:SCR_023280

Abstract

Animals exhibit innate behaviors that are stereotyped responses to specific evolutionarily relevant stimuli in the absence of prior learning or experience. The posterolateral cortical amygdala (plCoA) mediates innate attraction and aversion to odor. Here, we sought to define the circuit features of plCoA that give rise to innate attraction and aversion to odor in mice. First, we examined odor-evoked responses in these areas and found sparse encoding of odor identity, but not valence. We next considered a topographic organization and found that optogenetic stimulation of the anterior and posterior domains of plCoA elicits avoidance and attraction, respectively, suggesting a functional axis for valence. Using single-cell and spatial RNA sequencing, we identified the molecular cell types in plCoA, revealing an anteroposterior gradient in glutamatergic neurons that are sufficient and partially necessary for behavior. Finally, we identified topographically organized projections, whereby anterior neurons preferentially project to medial amygdala, and posterior neurons preferentially project to nucleus accumbens, which are respectively sufficient and necessary for innate attraction and aversion. Together, these data support a model whereby distinct, topographically distributed plCoA populations direct innate olfactory responses by signaling to divergent valence-specific targets, linking upstream olfactory identity to downstream valence behaviors, through a population code.

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

Code

No file of the authors' code could be read here: it is described below, and read at its source.

Zenodo 12601490

License: MIT
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
At the source:

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

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 0 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

The RNA sequencing data is deposited in GEO (accession number GSE270798). The code used to analyze all data and generate all graphs can be found online at Zenodo.

The following datasets were generated:

HoweJ 2024Control of innate olfactory valence by segregated cortical amygdala circuitsNCBI Gene Expression OmnibusGSE27079810.7554/eLife.104677PMC1300835941870253

HoweJ 2024Control of innate olfactory valence by segregated cortical amygdala circuitsZenodo10.5281/zenodo.12601490PMC1300835941870253

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

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 13 authors, 6 keywords, 11 MeSH terms, 9 funders, 91 references, 10 RRIDs.

Cite

This paper

Howe, J. R., Chan, C. L., Lee, D., Blanquart, M., Lee, J. H., Decoster, L., Romero, H. K., Zadina, A. N., Lemieux, M. E., Mills, F., Desplats, P. A., Tye, K. M., & Root, C. M. (2026). Control of innate olfactory valence by segregated cortical amygdala circuits. eLife, 14, RP104677. https://doi.org/10.7554/elife.104677

BibTeX

@article{howe2026control,
author = {Howe, James R and Chan, Chung Lung and Lee, Donghyung and Blanquart, Marlon and Lee, James H and Decoster, Laurine and Romero, Haylie K and Zadina, Abigail N and Lemieux, Mackenzie E and Mills, Fergil and Desplats, Paula A and Tye, Kay M and Root, Cory M},
title = {{Control of innate olfactory valence by segregated cortical amygdala circuits}},
journal = {eLife},
year = {2026},
month = mar,
volume = {14},
pages = {RP104677},
publisher = {eLife Sciences Publications, Ltd},
issn = {2050-084X},
doi = {10.7554/elife.104677},
url = {https://doi.org/10.7554/elife.104677},
pmid = {41870253},
pmcid = {PMC13008359}
}

RIS

TY - JOUR
AU - Howe, James R
AU - Chan, Chung Lung
AU - Lee, Donghyung
AU - Blanquart, Marlon
AU - Lee, James H
AU - Decoster, Laurine
AU - Romero, Haylie K
AU - Zadina, Abigail N
AU - Lemieux, Mackenzie E
AU - Mills, Fergil
AU - Desplats, Paula A
AU - Tye, Kay M
AU - Root, Cory M
TI - Control of innate olfactory valence by segregated cortical amygdala circuits
T2 - eLife
J2 - eLife
PY - 2026
DA - 2026/03/23
VL - 14
SP - RP104677
SN - 2050-084X
PB - eLife Sciences Publications, Ltd
DO - 10.7554/elife.104677
UR - https://doi.org/10.7554/elife.104677
LA - en
ER -

CSL-JSON

{
"id": "10.7554/elife.104677",
"type": "article-journal",
"title": "Control of innate olfactory valence by segregated cortical amygdala circuits",
"container-title": "eLife",
"author": [
{
"family": "Howe",
"given": "James R"
},
{
"family": "Chan",
"given": "Chung Lung"
},
{
"family": "Lee",
"given": "Donghyung"
},
{
"family": "Blanquart",
"given": "Marlon"
},
{
"family": "Lee",
"given": "James H"
},
{
"family": "Decoster",
"given": "Laurine"
},
{
"family": "Romero",
"given": "Haylie K"
},
{
"family": "Zadina",
"given": "Abigail N"
},
{
"family": "Lemieux",
"given": "Mackenzie E"
},
{
"family": "Mills",
"given": "Fergil"
},
{
"family": "Desplats",
"given": "Paula A"
},
{
"family": "Tye",
"given": "Kay M"
},
{
"family": "Root",
"given": "Cory M"
}
],
"container-title-short": "eLife",
"volume": "14",
"page": "RP104677",
"DOI": "10.7554/elife.104677",
"PMID": "41870253",
"PMCID": "PMC13008359",
"ISSN": "2050-084X",
"publisher": "eLife Sciences Publications, Ltd",
"URL": "https://doi.org/10.7554/elife.104677",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
23
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1007/s00213-022-06284-5 [code]
Thalamus sends information about arousal but not valence to the amygdala.
Journal: Psychopharmacology
In common: mouse, 2 references, 2 authors
[2] doi:10.7554/elife.90976
Transformation of valence signaling in a mouse striatopallidal circuit.
Journal: eLife
In common: systems, mouse, 5 references, author Cory M Root
[3] doi:10.1038/s41467-026-68313-7 [code]
Glutamatergic projection neurons in the basal forebrain underlie learned olfactory associational valence assignments.
Journal: Nature communications
In common: mouse, 8 references
[4] doi:10.1038/s41467-025-60360-w [code]
Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.
Journal: Nature communications
In common: mouse, 9 references
[5] doi:10.7554/elife.105955
Separable dorsal raphe dopamine projections mimic the facets of a loneliness-like state.
Journal: eLife
In common: mouse, 3 references, author Kay M Tye
[6] doi:10.1038/s41467-026-70356-9
A topographical organization in the primary olfactory cortex.
Journal: Nature communications
In common: systems, mouse, 5 references
[7] doi:10.1371/journal.pcbi.1014106 [code]
A multimodal spatial atlas of transcriptomic, morphological, and electrophysiological cell type densities in the mouse brain.
Journal: PLoS computational biology
In common: mouse, 7 references
[8] doi:10.1016/j.xgen.2025.100986 [code]
Cell-type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development.
Journal: Cell genomics
In common: mouse, 8 references
[9] doi:10.7554/elife.80470 [code]
Mapping odorant sensitivities reveals a sparse but structured representation of olfactory chemical space by sensory input to the mouse olfactory bulb.
Journal: eLife
In common: mouse, 5 references
[10] doi:10.1038/s41593-023-01469-3 [code]
Neuronal types in the mouse amygdala and their transcriptional response to fear conditioning.
Journal: Nature neuroscience
In common: mouse, 6 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Add the badge to the code's README

OSCR: the badge of this paper

If you are an author or a maintainer of this paper's code, you can add this badge. It says what OSCR knows of the paper (its code, its validated tracing map) and links the code to this page. Paste one of these snippets under the README's title. Keep the two marks around it, so that the badge can be replaced in place and is never added twice. OSCR changes nothing in your repository.

Markdown
<!-- oscr-badge:start -->
[![OSCR](https://openscicode.org/badge/doi/10.7554/elife.104677.svg)](https://openscicode.org/badge/doi/10.7554/elife.104677)
<!-- oscr-badge:end -->
reStructuredText
.. oscr-badge:start

.. image:: https://openscicode.org/badge/doi/10.7554/elife.104677.svg
   :target: https://openscicode.org/badge/doi/10.7554/elife.104677
   :alt: OSCR

.. oscr-badge:end
HTML
<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/doi/10.7554/elife.104677"><img src="https://openscicode.org/badge/doi/10.7554/elife.104677.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->

If you choose to, you can have the badge kept up to date for you, with oscr badge --write from the command line or with the GitHub Action in your repository's workflows. Every other form and option (a card, AsciiDoc, LaTeX, shields.io) is on the badge page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: code errors and mismatches between the code and the paper about this paper and its code, from readers and its authors, beside the paper and its tracing map.

Report a mismatch between the code and the paper · Report a code error (signed in)

Reproductions: reports from readers who ran the authors' code and did not get the paper's result, what they ran, with which environment, commit and data.

Report a reproduction failure (signed in)

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.