Transcriptional Response to Chronic Long-Access Fentanyl Self-Administration in Rat Habenula and Amygdala.
The 12 matches
- [1] § Materials and Methods Summary › Experiment Summary and RNA‐Seq Data Generation ↔ code/09_SRA/03_metadata.R, lines 1–55 · score 0.98 · inside sound attenuating, operant chambers housed, bilateral tissue punches, Ribosomal RNA depletion, Cayman Chemical, coronal slabs
- [2] § Results › Shared and Unique Gene Expression Changes in Hb and Amyg Following Chronic Fentanyl Intake ↔ code/06_GO_KEGG/01_GO_KEGG_Analyses.R, lines 548–592 · score 0.97 · gastric acid secretion, ECM receptor interaction, Parkinson disease, actin cytoskeleton, oxidative phosphorylation, glutamatergic synapse
- [3] § Results › Shared and Unique Gene Expression Changes in Hb and Amyg Following Chronic Fentanyl Intake ↔ code/05_DEA/01_Modeling.R, lines 477–532 · score 0.96 · Atp5mc2, Atp6v0e2, Atp6v1e1, Slc39a10, Col4a3, KEGG term
- [4] § Results › Shared and Unique Gene Expression Changes in Hb and Amyg Following Chronic Fentanyl Intake ↔ code/05_DEA/01_Modeling.R, lines 477–532 · score 0.91 · Cox6b1, Scn1a, Col9a3, Gria4, Grik1, Kcnj10
- [5] § Results › Shared and Unique Gene Expression Changes in Hb and Amyg Following Chronic Fentanyl Intake ↔ code/06_GO_KEGG/01_GO_KEGG_Analyses.R, lines 548–592 · score 0.87 · postsynaptic membrane potential, Col9a3, voltage gated, cation channels, Epha4, Gsn
- [6] § Materials and Methods Summary › Experiment Summary and RNA‐Seq Data Generation ↔ code/09_SRA/03_metadata.R, lines 1–55 · score 0.76 · bulk RNA sequencing, jugular catheters, house light, illumination, Drug, daily
- [7] § Materials and Methods Summary › Differential Gene Expression (DGE) ↔ code/06_GO_KEGG/01_GO_KEGG_Analyses.R, lines 73–188 · score 0.75 · enriched GO term, cellular components, Biological processes, molecular functions, enrichment, Amyg
- [8] § Results › Enrichment of Genes Associated With Fentanyl Intake in Human and Rodent Hb and Amyg Cell Types ↔ code/08_GSEA/01_enrich_DEGs_vs_cell_type_markers.R, lines 896–934 · score 0.65 · fine cell, DRD1, LAMP5, SATB2, nostrin, S14
- [9] § Results › Enrichment of Genes Associated With Fentanyl Intake in Human and Rodent Hb and Amyg Cell Types ↔ code/08_GSEA/01_enrich_DEGs_vs_cell_type_markers.R, lines 1295–1361 · score 0.63 · LHb.2, LHb.6, LHb.7, astrocytes, enriched, orthologous
- [10] § Materials and Methods Summary › Experiment Summary and RNA‐Seq Data Generation ↔ code/03_Data_preparation/01_build_objects.R, lines 47–85 · score 0.62 · tissue punches, library preparation, sequenced, RNA, brains, Amyg
- [11] § Materials and Methods Summary › RNA‐Seq Data Processing and Quality Control ↔ code/04_EDA/01_QCA.R, lines 2–87 · score 0.59 · quality control, expressed genes, QC metrics, RNA extraction, brain regions, filtered
- [12] § Materials and Methods Summary › Experiment Summary and RNA‐Seq Data Generation ↔ code/04_EDA/03_Explore_gene_level_effects.R, lines 2–55 · score 0.54 · linear regression, infusion slopes, mg, hour, RNA, intake
Paper
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The authors' code
R · 1,005 lines · 57 KB · MIT · 3 matches
01_GO_KEGG_Analyses.R at commit 4284eba, under MIT · at the source
Overview
- Department of Psychological and Brain Sciences, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, Maryland, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
Abstract
Fentanyl is a potent synthetic opioid associated with overdose. However, little is known about fentanyl‐induced molecular adaptations in the habenula and amygdala, two brain regions implicated in opioid use and withdrawal. We performed bulk RNA‐sequencing in the rat habenula and amygdala to identify transcriptomic changes associated with fentanyl intake. Male rats self‐administered intravenous saline or fentanyl over 22–24 days. Ninety minutes following the final session, brains were collected for transcriptomic profiling. In Hb, we identified 453 differentially expressed genes (DEGs) between saline and fentanyl rats, with upregulated genes associated with synaptic transmission and ionic conductance. In the amygdala, we identified 3041 fentanyl‐associated DEGs with upregulated genes implicated in metabolic and vesicular functions. Downregulated genes in both regions were enriched for extracellular matrix functions. Integration of DEGs with single‐cell RNA‐sequencing data from rodents and humans revealed that fentanyl DEGs were enriched in specific habenula and amygdala cell type markers. Furthermore, fentanyl downregulated DEGs in the amygdala were enriched in genes associated with the risk for substance use disorders. Together, we define how fentanyl intake alters transcriptional programs in the rat habenula and amygdala, and we link these changes to specific human cell types and risk genes for neuropsychiatric disorders and addiction.
Reproduced under the paper's license (CC BY), from the paper cited above.
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LieberInstitute/fentanyl_rat_hb_amy
4284ebac39e53fe23aea2a23812dc71441c14e10, 15 July 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
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01_transfer_data/ — Shell, 51 lines, shown from its source01_psomagen_data.sh - code/
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Zenodo 17573970
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
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Data
No dataset and no data link were found in the paper.
Data Availability Statement
The source FASTQ files are publicly available from the NCBI Sequence Read Archive BioProject PRJNA1179901. All analysis code is available at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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Version 2, 28 September 2026
- Authors: added Ege A Yalcinbas (0000-0002-9480-7192); Emma Chaloux‐Pinette (0000-0002-6832-6862); Nicholas J Eagles (0000-0002-9808-5254); Michael S Totty (0000-0002-9292-8556); Patricia H Janak (0000-0002-3333-9049); Kristen R Maynard (0000-0003-0031-8468); removed Ege A Yalcinbas; Emma Chaloux‐Pinette; Nicholas J Eagles; Michael S Totty; Patricia H Janak; Kristen R Maynard
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 11 MeSH terms, 5 funders, 103 references.
Cite
This paper
Magnard, R., Gonzalez‐Padilla, D., Yalcinbas, E. A., Chaloux‐Pinette, E., Eagles, N. J., Totty, M. S., Janak, P. H., Collado‐Torres, L., & Maynard, K. R. (2026). Transcriptional Response to Chronic Long-Access Fentanyl Self-Administration in Rat Habenula and Amygdala. Addiction biology, 31(7), e70179. https://
BibTeX
@article{magnard2026tran
author = {Magnard, Robin and Gonzalez‐Padilla, Daianna and Yalcinbas, Ege A and Chaloux‐Pinette, Emma and Eagles, Nicholas J and Totty, Michael S and Janak, Patricia H and Collado‐Torres, Leonardo and Maynard, Kristen R},
title = {{Transcriptional Response to Chronic Long-Access Fentanyl Self-Administration in Rat Habenula and Amygdala}},
journal = {Addiction biology},
year = {2026},
month = jul,
volume = {31},
number = {7},
pages = {e70179},
publisher = {Wiley},
issn = {1355-6215},
doi = {10.1111/
url = {https://
pmid = {42444546},
pmcid = {PMC13366401}
}
RIS
TY - JOUR
AU - Magnard, Robin
AU - Gonzalez‐Padilla, Daianna
AU - Yalcinbas, Ege A
AU - Chaloux‐Pinette, Emma
AU - Eagles, Nicholas J
AU - Totty, Michael S
AU - Janak, Patricia H
AU - Collado‐Torres, Leonardo
AU - Maynard, Kristen R
TI - Transcriptional Response to Chronic Long-Access Fentanyl Self-Administration in Rat Habenula and Amygdala
T2 - Addiction biology
J2 - Addict Biol
PY - 2026
DA - 2026/
VL - 31
IS - 7
SP - e70179
SN - 1355-6215
PB - Wiley
DO - 10.1111/
UR - https://
LA - en
ER -
CSL-JSON
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