{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T06:13:38Z","timestamp":1789020818901,"version":"build-2803163510"},"reference-count":111,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T00:00:00Z","timestamp":1747008000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T00:00:00Z","timestamp":1747008000000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T00:00:00Z","timestamp":1747008000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018231","name":"Aligning Science Across Parkinson's","doi-asserted-by":"publisher","award":["ASAP020600"],"award-info":[{"award-number":["ASAP020600"]}],"id":[{"id":"10.13039\/100018231","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01NS119690-01"],"award-info":[{"award-number":["1R01NS119690-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P50 DA044121-01A1"],"award-info":[{"award-number":["P50 DA044121-01A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 NS097901"],"award-info":[{"award-number":["R01 NS097901"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1F31NS115524-01A1"],"award-info":[{"award-number":["1F31NS115524-01A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["PJT-183760"],"award-info":[{"award-number":["PJT-183760"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100032960","name":"Healthy Brains Healthy Lives","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100032960","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100009307","name":"Parkinson Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009307","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002661","name":"Fonds De La Recherche Scientifique - FNRS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    Several studies have revealed that midbrain dopamine (DA) neurons, even within a single neuroanatomical area, display heterogeneous properties. In parallel, studies using singlecell profiling techniques have begun to cluster DA neurons into subtypes based on their molecular signatures. Recent work has shown that molecularly defined DA subtypes within the substantia nigra (SNc) display distinctive anatomic and functional properties, and differential vulnerability in Parkinson\u2019s disease (PD). Based on these provocative results, a granular understanding of these putative subtypes and their alterations in PD models, is imperative. We developed an optimized pipeline for single-nuclear RNA sequencing (snRNA-seq) and generated a high-resolution hierarchically organized map revealing 20 molecularly distinct DA neuron subtypes belonging to three main families. We integrated this data with spatial MERFISH technology to map, with high definition, the location of these subtypes in the mouse midbrain, revealing heterogeneity even within neuroanatomical sub-structures. Finally, we demonstrate that in the preclinical LRRK2\n                    <jats:sup>G2019S<\/jats:sup>\n                    knock-in mouse model of PD, subtype organization and proportions are preserved. Transcriptional alterations occur in many subtypes including those localized to the ventral tier SNc, where differential expression is observed in synaptic pathways, which might account for previously described DA release deficits in this model. Our work provides an advancement of current taxonomic schemes of the mouse midbrain DA neuron subtypes, a high-resolution view of their spatial locations, and their alterations in a prodromal mouse model of PD.\n                  <\/jats:p>","DOI":"10.7554\/elife.101035","type":"journal-article","created":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T10:25:14Z","timestamp":1732184714000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.101035","source":"Crossref","is-referenced-by-count":28,"title":["Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019S model of Parkinson\u2019s disease"],"prefix":"10.7554","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1760-6549","authenticated-orcid":true,"given":"Zachary","family":"Gaertner","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/000e0be47","id-type":"ROR","asserted-by":"publisher"}],"name":"Northwestern University Feinberg School of Medicine, Dept of Neurology","place":["Chicago, United States"]},{"id":[{"id":"https:\/\/ror.org\/000e0be47","id-type":"ROR","asserted-by":"publisher"}],"name":"Northwestern University, Dept of Neurobiology","place":["Evanston, United States"]},{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network","place":["Chevy Chase, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Cameron","family":"Oram","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01pxwe438","id-type":"ROR","asserted-by":"publisher"}],"name":"McGill University (Montreal Neurological Institute), Faculty of Medicine and Health Sciences, Dept of Neurology and Neurosurgery","place":["Montreal, Canada"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4141-6064","authenticated-orcid":true,"given":"Amanda","family":"Schneeweis","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/000e0be47","id-type":"ROR","asserted-by":"publisher"}],"name":"Northwestern University Feinberg School of Medicine, Dept of Neurology","place":["Chicago, United States"]},{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network","place":["Chevy Chase, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"project-administration","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7368-1562","authenticated-orcid":true,"given":"Elan","family":"Schonfeld","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/000e0be47","id-type":"ROR","asserted-by":"publisher"}],"name":"Northwestern University Feinberg School of Medicine, Dept of Neurology","place":["Chicago, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Cyril","family":"Bolduc","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01pxwe438","id-type":"ROR","asserted-by":"publisher"}],"name":"McGill University (Montreal Neurological Institute), Faculty of Medicine and Health Sciences, Dept of Neurology and Neurosurgery","place":["Montreal, Canada"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5666-5173","authenticated-orcid":true,"given":"Chuyu","family":"Chen","sequence":"additional","affiliation":[{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network","place":["Chevy Chase, United States"]},{"id":[{"id":"https:\/\/ror.org\/04fzwnh64","id-type":"ROR","asserted-by":"publisher"}],"name":"Northwestern University Feinberg School of Medicine, Dept of Pharmacology","place":["Chicago, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"data-curation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2576-5918","authenticated-orcid":true,"given":"Daniel","family":"Dombeck","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/000e0be47","id-type":"ROR","asserted-by":"publisher"}],"name":"Northwestern University, Dept of Neurobiology","place":["Evanston, United States"]},{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network","place":["Chevy Chase, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2569-4200","authenticated-orcid":true,"given":"Loukia","family":"Parisiadou","sequence":"additional","affiliation":[{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network","place":["Chevy Chase, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1039-4985","authenticated-orcid":true,"given":"Jean-Francois","family":"Poulin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01pxwe438","id-type":"ROR","asserted-by":"publisher"}],"name":"McGill University (Montreal Neurological Institute), Faculty of Medicine and Health Sciences, Dept of Neurology and Neurosurgery","place":["Montreal, Canada"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0713-2140","authenticated-orcid":true,"given":"Rajeshwar","family":"Awatramani","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/000e0be47","id-type":"ROR","asserted-by":"publisher"}],"name":"Northwestern University Feinberg School of Medicine, Dept of Neurology","place":["Chicago, United States"]},{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network","place":["Chevy Chase, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2025,5,12]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"3714","DOI":"10.1016\/j.febslet.2015.10.022","type":"journal-article","article-title":"Molecular heterogeneity of midbrain dopaminergic neurons--Moving toward single cell resolution","volume":"589","author":"Anderegg","year":"2015","journal-title":"FEBS Letters"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1016\/j.cell.2005.10.037","type":"journal-article","article-title":"Identification of intrinsic determinants of midbrain dopamine neurons","volume":"124","author":"Andersson","year":"2006","journal-title":"Cell"},{"key":"bib3","doi-asserted-by":"publisher","DOI":"10.1016\/j.phrs.2019.104515","type":"journal-article","article-title":"miR-124 and Parkinson\u2019s disease: A biomarker with therapeutic potential","volume":"150","author":"Angelopoulou","year":"2019","journal-title":"Pharmacological Research"},{"key":"bib4","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2024.114080","type":"journal-article","article-title":"Distributional coding of associative learning in discrete populations of midbrain dopamine neurons","volume":"43","author":"Avvisati","year":"2024","journal-title":"Cell Reports"},{"key":"bib5","type":"software","article-title":"Gaertner_Oram_etal","volume-title":"Software Heritage","author":"AwatramaniLab","year":"2025","unstructured":"AwatramaniLab. 2025. Gaertner_Oram_etal. Software Heritage. swh:1:rev:cc4374e0b87b121d2117707467cd79a80e0bb44d. https:\/\/archive.softwareheritage.org\/swh:1:dir:acdb8187f0bafd685026137a864bc7ee8f7c70da;origin=https:\/\/github.com\/AwatramaniLab\/Gaertner_Oram_etal;visit=swh:1:snp:9ffbc4187c0915f4adabbe0dcfa34dd7e374ec66;anchor=swh:1:rev:cc4374e0b87b121d2117707467cd79a80e0bb44d."},{"key":"bib6","doi-asserted-by":"publisher","first-page":"1762","DOI":"10.1038\/s41593-023-01401-9","type":"journal-article","article-title":"Unique functional responses differentially map onto genetic subtypes of dopamine neurons","volume":"26","author":"Azcorra","year":"2023","journal-title":"Nature Neuroscience"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1016\/j.cell.2015.07.015","type":"journal-article","article-title":"Circuit architecture of VTA dopamine neurons revealed by systematic input-output mapping","volume":"162","author":"Beier","year":"2015","journal-title":"Cell"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.tins.2007.03.006","type":"journal-article","article-title":"Dopamine neuron systems in the brain: an update","volume":"30","author":"Bj\u00f6rklund","year":"2007","journal-title":"Trends in Neurosciences"},{"key":"bib9","doi-asserted-by":"publisher","DOI":"10.1186\/1749-8104-6-29","type":"journal-article","article-title":"Temporal-spatial changes in Sonic Hedgehog expression and signaling reveal different potentials of ventral mesencephalic progenitors to populate distinct ventral midbrain nuclei","volume":"6","author":"Blaess","year":"2011","journal-title":"Neural Development"},{"key":"bib10","doi-asserted-by":"publisher","first-page":"2140","DOI":"10.1016\/j.cub.2021.02.061","type":"journal-article","article-title":"Increased LRRK2 kinase activity alters neuronal autophagy by disrupting the axonal transport of autophagosomes","volume":"31","author":"Boecker","year":"2021","journal-title":"Current Biology"},{"key":"bib11","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1007\/s00401-009-0601-5","type":"journal-article","article-title":"Oligodendrocytes: biology and pathology","volume":"119","author":"Bradl","year":"2010","journal-title":"Acta Neuropathologica"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"4894","DOI":"10.1073\/pnas.0811507106","type":"journal-article","article-title":"Phasic excitation of dopamine neurons in ventral VTA by noxious stimuli","volume":"106","author":"Brischoux","year":"2009","journal-title":"PNAS"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/s43587-022-00335-4","type":"journal-article","article-title":"Cell-type-specific aging clocks to quantify aging and rejuvenation in neurogenic regions of the brain","volume":"3","author":"Buckley","year":"2023","journal-title":"Nature Aging"},{"key":"bib14","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaa6090","type":"journal-article","article-title":"RNA imaging: Spatially resolved, highly multiplexed RNA profiling in single cells","volume":"348","author":"Chen","year":"2015","journal-title":"Science"},{"key":"bib15","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.58997","type":"journal-article","article-title":"Pathway-specific dysregulation of striatal excitatory synapses by LRRK2 mutations","volume":"9","author":"Chen","year":"2020","journal-title":"eLife"},{"key":"bib16","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms9255","type":"journal-article","article-title":"LRRK2 G2019S mutation attenuates microglial motility by inhibiting focal adhesion kinase","volume":"6","author":"Choi","year":"2015","journal-title":"Nature Communications"},{"key":"bib17","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02584-9","type":"journal-article","article-title":"Comparison and evaluation of statistical error models for scRNA-seq","volume":"23","author":"Choudhary","year":"2022","journal-title":"Genome Biology"},{"key":"bib18","doi-asserted-by":"publisher","DOI":"10.1101\/2024.02.28.582356","type":"preprint","article-title":"Proportion and distribution of neurotransmitter-defined cell types in the ventral tegmental area and substantia nigra pars compacta","volume-title":"bioRxiv","author":"Conrad","year":"2024"},{"key":"bib19","doi-asserted-by":"publisher","DOI":"10.1038\/s41531-017-0010-8","type":"journal-article","article-title":"LRRK2 levels in immune cells are increased in Parkinson\u2019s disease","volume":"3","author":"Cook","year":"2017","journal-title":"NPJ Parkinson\u2019s Disease"},{"key":"bib20","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1038\/s41583-019-0189-2","type":"journal-article","article-title":"Striatal circuits for reward learning and decision-making","volume":"20","author":"Cox","year":"2019","journal-title":"Nature Reviews. Neuroscience"},{"key":"bib21","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03282-0","type":"journal-article","article-title":"Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor","volume":"9","author":"Crow","year":"2018","journal-title":"Nature Communications"},{"key":"bib22","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1093\/brain\/122.8.1421","type":"journal-article","article-title":"The substantia nigra of the human brain. I. Nigrosomes and the nigral matrix, a compartmental organization based on calbindin D(28K) immunohistochemistry","volume":"122","author":"Damier","year":"1999","journal-title":"Brain"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1038\/nature25457","type":"journal-article","article-title":"Dopamine neuron activity before action initiation gates and invigorates future movements","volume":"554","author":"da Silva","year":"2018","journal-title":"Nature"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1016\/j.brainresrev.2007.10.005","type":"journal-article","article-title":"Glutamate in dopamine neurons: synaptic versus diffuse transmission","volume":"58","author":"Descarries","year":"2008","journal-title":"Brain Research Reviews"},{"key":"bib25","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aar5429","type":"journal-article","article-title":"LRRK2 activation in idiopathic Parkinson\u2019s disease","volume":"10","author":"Di Maio","year":"2018","journal-title":"Science Translational Medicine"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1038\/s41586-019-1261-9","type":"journal-article","article-title":"Specialized coding of sensory, motor and cognitive variables in VTA dopamine neurons","volume":"570","author":"Engelhard","year":"2019","journal-title":"Nature"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"3704","DOI":"10.1523\/JNEUROSCI.0117-17.2017","type":"journal-article","article-title":"Dopamine inhibition differentially controls excitability of substantia nigra dopamine neuron subpopulations through T-type calcium channels","volume":"37","author":"Evans","year":"2017","journal-title":"The Journal of Neuroscience"},{"key":"bib28","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1007\/s00429-011-0349-2","type":"journal-article","article-title":"A cytoarchitectonic and chemoarchitectonic analysis of the dopamine cell groups in the substantia nigra, ventral tegmental area, and retrorubral field in the mouse","volume":"217","author":"Fu","year":"2012","journal-title":"Brain Structure & Function"},{"key":"bib29","doi-asserted-by":"publisher","DOI":"10.1016\/j.nbd.2022.105925","type":"journal-article","article-title":"Molecular heterogeneity in the substantia nigra: A roadmap for understanding PD motor pathophysiology","volume":"175","author":"Gaertner","year":"2022","journal-title":"Neurobiology of Disease"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1038\/s41583-022-00669-3","type":"journal-article","article-title":"Development, wiring and function of dopamine neuron subtypes","volume":"24","author":"Garritsen","year":"2023","journal-title":"Nature Reviews. Neuroscience"},{"key":"bib31","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1038\/s41586-021-04059-0","type":"journal-article","article-title":"Disruption of mitochondrial complex I induces progressive parkinsonism","volume":"599","author":"Gonz\u00e1lez-Rodr\u00edguez","year":"2021","journal-title":"Nature"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.nbd.2006.04.001","type":"journal-article","article-title":"Kinase activity is required for the toxic effects of mutant LRRK2\/dardarin","volume":"23","author":"Greggio","year":"2006","journal-title":"Neurobiology of Disease"},{"key":"bib33","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2019.01555","type":"journal-article","article-title":"MiR-124 and the underlying therapeutic promise of neurodegenerative disorders","volume":"10","author":"Han","year":"2019","journal-title":"Frontiers in Pharmacology"},{"key":"bib34","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","type":"journal-article","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nature Biotechnology"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1016\/j.neuron.2019.11.024","type":"journal-article","article-title":"Synergy of distinct dopamine projection populations in behavioral reinforcement","volume":"105","author":"Heymann","year":"2020","journal-title":"Neuron"},{"key":"bib36","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1016\/j.ajhg.2018.02.001","type":"journal-article","article-title":"Single-Cell RNA-Seq of mouse dopaminergic neurons informs candidate gene selection for sporadic Parkinson disease","volume":"102","author":"Hook","year":"2018","journal-title":"American Journal of Human Genetics"},{"key":"bib37","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/nature18942","type":"journal-article","article-title":"Rapid signalling in distinct dopaminergic axons during locomotion and reward","volume":"535","author":"Howe","year":"2016","journal-title":"Nature"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"5365","DOI":"10.1093\/hmg\/ddw352","type":"journal-article","article-title":"Human R1441C LRRK2 regulates the synaptic vesicle proteome and phosphoproteome in a Drosophila model of Parkinson\u2019s disease","volume":"25","author":"Islam","year":"2016","journal-title":"Human Molecular Genetics"},{"key":"bib39","doi-asserted-by":"publisher","DOI":"10.1101\/2023.07.26.550355","type":"preprint","article-title":"Cell-type specific molecular signatures of aging revealed in a brain-wide transcriptomic cell-type atlas","volume-title":"bioRxiv","author":"Jin","year":"2023"},{"key":"bib40","doi-asserted-by":"publisher","first-page":"19185","DOI":"10.1073\/pnas.0904285106","type":"journal-article","article-title":"Spatiotemporally separable Shh domains in the midbrain define distinct dopaminergic progenitor pools","volume":"106","author":"Joksimovic","year":"2009","journal-title":"PNAS"},{"key":"bib41","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1038\/s41593-022-01061-1","type":"journal-article","article-title":"Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson\u2019s disease","volume":"25","author":"Kamath","year":"2022","journal-title":"Nature Neuroscience"},{"key":"bib42","doi-asserted-by":"publisher","DOI":"10.1101\/2024.01.15.575737","type":"preprint","article-title":"Loss of Primary Cilia and Dopaminergic Neuroprotection in Pathogenic LRRK2-Driven and Idiopathic Parkinson\u2019s Disease","volume-title":"bioRxiv","author":"Khan","year":"2024"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1056\/NEJM198804073181402","type":"journal-article","article-title":"Uneven pattern of dopamine loss in the striatum of patients with idiopathic Parkinson\u2019s disease","volume":"318","author":"Kish","year":"1988","journal-title":"New England Journal of Medicine"},{"key":"bib44","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.neuron.2019.05.002","type":"journal-article","article-title":"SynGO: an evidence-based, expert-curated knowledge base for the synapse","volume":"103","author":"Koopmans","year":"2019","journal-title":"Neuron"},{"key":"bib45","doi-asserted-by":"publisher","first-page":"2419","DOI":"10.1093\/brain\/awt192","type":"journal-article","article-title":"Disease duration and the integrity of the nigrostriatal system in Parkinson\u2019s disease","volume":"136","author":"Kordower","year":"2013","journal-title":"Brain"},{"key":"bib46","doi-asserted-by":"publisher","DOI":"10.1523\/ENEURO.0152-18.2018","type":"journal-article","article-title":"Combinatorial Expression of Grp and Neurod6 defines dopamine neuron populations with distinct projection patterns and disease vulnerability","volume":"5","author":"Kramer","year":"2018","journal-title":"eNeuro"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1016\/j.cell.2016.09.027","type":"journal-article","article-title":"Molecular diversity of midbrain development in mouse, human, and stem cells","volume":"167","author":"La Manno","year":"2016","journal-title":"Cell"},{"key":"bib48","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1016\/j.neuron.2008.01.022","type":"journal-article","article-title":"Unique properties of mesoprefrontal neurons within a dual mesocorticolimbic dopamine system","volume":"57","author":"Lammel","year":"2008","journal-title":"Neuron"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/s41586-023-06818-7","type":"journal-article","article-title":"The molecular cytoarchitecture of the adult mouse brain","volume":"624","author":"Langlieb","year":"2023","journal-title":"Nature"},{"key":"bib50","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1016\/j.cell.2015.07.014","type":"journal-article","article-title":"Intact-brain analyses reveal distinct information carried by SNc dopamine subcircuits","volume":"162","author":"Lerner","year":"2015","journal-title":"Cell"},{"key":"bib51","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-27729-z","type":"journal-article","article-title":"Zero-preserving imputation of single-cell RNA-seq data","volume":"13","author":"Linderman","year":"2022","journal-title":"Nature Communications"},{"key":"bib52","doi-asserted-by":"publisher","first-page":"5299","DOI":"10.1093\/hmg\/ddv249","type":"journal-article","article-title":"Selective expression of Parkinson\u2019s disease-related Leucine-rich repeat kinase 2 G2019S missense mutation in midbrain dopaminergic neurons impairs dopamine release and dopaminergic gene expression","volume":"24","author":"Liu","year":"2015","journal-title":"Human Molecular Genetics"},{"key":"bib53","doi-asserted-by":"publisher","first-page":"3196","DOI":"10.1080\/15548627.2020.1850008","type":"journal-article","article-title":"Aberrant mitochondrial morphology and function associated with impaired mitophagy and DNM1L-MAPK\/ERK signaling are found in aged mutant Parkinsonian LRRK2R1441G mice","volume":"17","author":"Liu","year":"2021","journal-title":"Autophagy"},{"key":"bib54","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1016\/j.nbd.2012.07.017","type":"journal-article","article-title":"LRRK2 expression is enriched in the striosomal compartment of mouse striatum","volume":"48","author":"Mandemakers","year":"2012","journal-title":"Neurobiology of Disease"},{"key":"bib55","doi-asserted-by":"publisher","first-page":"7128","DOI":"10.1523\/JNEUROSCI.3314-15.2016","type":"journal-article","article-title":"Altered development of synapse structure and function in striatum caused by Parkinson\u2019s disease-linked LRRK2-G2019S mutation","volume":"36","author":"Matikainen-Ankney","year":"2016","journal-title":"The Journal of Neuroscience"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1038\/nature08028","type":"journal-article","article-title":"Two types of dopamine neuron distinctly convey positive and negative motivational signals","volume":"459","author":"Matsumoto","year":"2009","journal-title":"Nature"},{"key":"bib57","doi-asserted-by":"publisher","DOI":"10.1038\/s41531-024-00818-8","type":"journal-article","article-title":"Relative sparing of dopaminergic terminals in the caudate nucleus is a feature of rest tremor in Parkinson\u2019s disease","volume":"10","author":"Mendon\u00e7a","year":"2024","journal-title":"NPJ Parkinson\u2019s Disease"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"1421","DOI":"10.1038\/s41593-018-0222-1","type":"journal-article","article-title":"Dopamine neurons projecting to the posterior striatum reinforce avoidance of threatening stimuli","volume":"21","author":"Menegas","year":"2018","journal-title":"Nature Neuroscience"},{"key":"bib59","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1016\/j.neuroscience.2014.05.032","type":"journal-article","article-title":"Glutamate neurons within the midbrain dopamine regions","volume":"282","author":"Morales","year":"2014","journal-title":"Neuroscience"},{"key":"bib60","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/nrn.2016.165","type":"journal-article","article-title":"Ventral tegmental area: cellular heterogeneity, connectivity and behaviour","volume":"18","author":"Morales","year":"2017","journal-title":"Nature Reviews. Neuroscience"},{"key":"bib61","doi-asserted-by":"publisher","first-page":"2017","DOI":"10.1212\/WNL.0b013e3181ff9685","type":"journal-article","article-title":"Mitochondrial impairment in patients with Parkinson disease with the G2019S mutation in LRRK2","volume":"75","author":"Mortiboys","year":"2010","journal-title":"Neurology"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1016\/S1474-4422(19)30320-5","type":"journal-article","article-title":"Identification of novel risk loci, causal insights, and heritable risk for Parkinson\u2019s disease: a meta-analysis of genome-wide association studies","volume":"18","author":"Nalls","year":"2019","journal-title":"The Lancet. Neurology"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"5576","DOI":"10.1073\/pnas.1717590115","type":"journal-article","article-title":"LRRK2 phosphorylation of auxilin mediates synaptic defects in dopaminergic neurons from patients with Parkinson\u2019s disease","volume":"115","author":"Nguyen","year":"2018","journal-title":"PNAS"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1242\/dev.144949","type":"journal-article","article-title":"A novel floor plate boundary defined by adjacent En1 and Dbx1 microdomains distinguishes midbrain dopamine and hypothalamic neurons","volume":"144","author":"Nouri","year":"2017","journal-title":"Development"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"3374","DOI":"10.1093\/bioinformatics\/btab209","type":"journal-article","article-title":"ShinyCell: simple and sharable visualization of single-cell gene expression data","volume":"37","author":"Ouyang","year":"2021","journal-title":"Bioinformatics"},{"key":"bib66","doi-asserted-by":"publisher","DOI":"10.1016\/j.nbd.2021.105390","type":"journal-article","article-title":"Dopamine neuron-specific LRRK2 G2019S effects on gene expression revealed by translatome profiling","volume":"155","author":"Pallos","year":"2021","journal-title":"Neurobiology of Disease"},{"key":"bib67","doi-asserted-by":"publisher","first-page":"11366","DOI":"10.1523\/JNEUROSCI.0964-17.2017","type":"journal-article","article-title":"Parkinson\u2019s disease-associated LRRK2 hyperactive kinase mutant disrupts synaptic vesicle trafficking in ventral midbrain neurons","volume":"37","author":"Pan","year":"2017","journal-title":"The Journal of Neuroscience"},{"key":"bib68","doi-asserted-by":"publisher","first-page":"1018","DOI":"10.1016\/j.celrep.2014.07.016","type":"journal-article","article-title":"Sox6 and Otx2 control the specification of substantia nigra and ventral tegmental area dopamine neurons","volume":"8","author":"Panman","year":"2014","journal-title":"Cell Reports"},{"key":"bib69","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/nn.3636","type":"journal-article","article-title":"LRRK2 regulates synaptogenesis and dopamine receptor activation through modulation of PKA activity","volume":"17","author":"Parisiadou","year":"2014","journal-title":"Nature Neuroscience"},{"key":"bib70","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.109975","type":"journal-article","article-title":"Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins","volume":"37","author":"Pereira Luppi","year":"2021","journal-title":"Cell Reports"},{"key":"bib71","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2022.110616","type":"journal-article","article-title":"An atlas of transcriptionally defined cell populations in the rat ventral tegmental area","volume":"39","author":"Phillips","year":"2022","journal-title":"Cell Reports"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1111\/jnc.15240","type":"journal-article","article-title":"LRRK2 at the pre-synaptic site: A 16-years perspective","volume":"157","author":"Pischedda","year":"2021","journal-title":"Journal of Neurochemistry"},{"key":"bib73","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1016\/j.celrep.2014.10.008","type":"journal-article","article-title":"Defining midbrain dopaminergic neuron diversity by single-cell gene expression profiling","volume":"9","author":"Poulin","year":"2014","journal-title":"Cell Reports"},{"key":"bib74","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1038\/s41593-018-0203-4","type":"journal-article","article-title":"Mapping projections of molecularly defined dopamine neuron subtypes using intersectional genetic approaches","volume":"21","author":"Poulin","year":"2018","journal-title":"Nature Neuroscience"},{"key":"bib75","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.tins.2020.01.004","type":"journal-article","article-title":"Classification of midbrain dopamine neurons using single-cell gene expression profiling approaches","volume":"43","author":"Poulin","year":"2020","journal-title":"Trends in Neurosciences"},{"key":"bib76","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1016\/j.cell.2018.07.028","type":"journal-article","article-title":"Molecular diversity and specializations among the cells of the adult mouse brain","volume":"174","author":"Saunders","year":"2018","journal-title":"Cell"},{"key":"bib77","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf4740","type":"journal-article","article-title":"Striatal dopamine mediates hallucination-like perception in mice","volume":"372","author":"Schmack","year":"2021","journal-title":"Science"},{"key":"bib78","doi-asserted-by":"publisher","DOI":"10.1126\/science.add7046","type":"journal-article","article-title":"Transcriptomic diversity of cell types across the adult human brain","volume":"382","author":"Siletti","year":"2023","journal-title":"Science"},{"key":"bib79","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1016\/j.brainres.2018.06.010","type":"journal-article","article-title":"LRRK2 and mitochondria: Recent advances and current views","volume":"1702","author":"Singh","year":"2019","journal-title":"Brain Research"},{"key":"bib80","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.67604","type":"journal-article","article-title":"Pharmacological rescue of impaired mitophagy in Parkinson\u2019s disease-related LRRK2 G2019S knock-in mice","volume":"10","author":"Singh","year":"2021","journal-title":"eLife"},{"key":"bib81","doi-asserted-by":"publisher","DOI":"10.3390\/cells11010169","type":"journal-article","article-title":"LRRK2 at striatal synapses: cell-type specificity and mechanistic insights","volume":"11","author":"Skelton","year":"2022","journal-title":"Cells"},{"key":"bib82","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1016\/j.celrep.2016.05.067","type":"journal-article","article-title":"Genetic isolation of hypothalamic neurons that regulate context-specific male social behavior","volume":"16","author":"Soden","year":"2016","journal-title":"Cell Reports"},{"key":"bib83","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1016\/j.neuron.2016.09.037","type":"journal-article","article-title":"A LRRK2-Dependent EndophilinA Phosphoswitch Is Critical for Macroautophagy at Presynaptic Terminals","volume":"92","author":"Soukup","year":"2016","journal-title":"Neuron"},{"key":"bib84","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","type":"journal-article","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"bib85","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nrn.2016.178","type":"journal-article","article-title":"Selective neuronal vulnerability in Parkinson disease","volume":"18","author":"Surmeier","year":"2017","journal-title":"Nature Reviews. Neuroscience"},{"key":"bib86","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-43213-2","type":"journal-article","article-title":"A primate nigrostriatal atlas of neuronal vulnerability and resilience in A model of Parkinson\u2019s disease","volume":"14","author":"Tang","year":"2023","journal-title":"Nature Communications"},{"key":"bib87","doi-asserted-by":"publisher","DOI":"10.1038\/s41531-023-00544-7","type":"journal-article","article-title":"Perspective on the current state of the LRRK2 field","volume":"9","author":"Taymans","year":"2023","journal-title":"NPJ Parkinson\u2019s Disease"},{"key":"bib88","doi-asserted-by":"publisher","first-page":"2404","DOI":"10.1016\/j.celrep.2018.07.101","type":"journal-article","article-title":"Mitochondrial complex I activity is required for maximal autophagy","volume":"24","author":"Thomas","year":"2018","journal-title":"Cell Reports"},{"key":"bib89","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-08453-1","type":"journal-article","article-title":"Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development","volume":"10","author":"Tiklov\u00e1","year":"2019","journal-title":"Nature Communications"},{"key":"bib90","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/j.tibs.2021.10.003","type":"journal-article","article-title":"Closing the structure-to-function gap for LRRK2","volume":"47","author":"Tokars","year":"2022","journal-title":"Trends in Biochemical Sciences"},{"key":"bib91","doi-asserted-by":"publisher","DOI":"10.1038\/s41419-017-0221-2","type":"journal-article","article-title":"Dopamine D2 receptor-mediated neuroprotection in a G2019S Lrrk2 genetic model of Parkinson\u2019s disease","volume":"9","author":"Tozzi","year":"2018","journal-title":"Cell Death & Disease"},{"key":"bib92","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1038\/nrn.2015.21","type":"journal-article","article-title":"Mechanisms and functions of GABA co-release","volume":"17","author":"Tritsch","year":"2016","journal-title":"Nature Reviews. Neuroscience"},{"key":"bib93","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/B978-0-444-63425-2.00006-4","type":"journal-article","article-title":"The multilingual nature of dopamine neurons","volume":"211","author":"Trudeau","year":"2014","journal-title":"Progress in Brain Research"},{"key":"bib94","doi-asserted-by":"publisher","first-page":"2465","DOI":"10.1002\/cne.23583","type":"journal-article","article-title":"Differential LRRK2 expression in the cortex, striatum, and substantia nigra in transgenic and nontransgenic rodents","volume":"522","author":"West","year":"2014","journal-title":"The Journal of Comparative Neurology"},{"key":"bib95","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0","type":"journal-article","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biology"},{"key":"bib96","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.1016\/j.celrep.2019.06.095","type":"journal-article","article-title":"Distinct connectivity and functionality of aldehyde dehydrogenase 1a1-positive nigrostriatal dopaminergic neurons in motor learning","volume":"28","author":"Wu","year":"2019","journal-title":"Cell Reports"},{"key":"bib97","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-022-04136-8","type":"journal-article","article-title":"R1441C and G2019S LRRK2 knockin mice have distinct striatal molecular, physiological, and behavioral alterations","volume":"5","author":"Xenias","year":"2022","journal-title":"Communications Biology"},{"key":"bib98","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.89482","type":"journal-article","article-title":"Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model","volume":"12","author":"Yaghmaeian Salmani","year":"2024","journal-title":"eLife"},{"key":"bib99","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1016\/0006-8993(90)91236-a","type":"journal-article","article-title":"Relative sparing in Parkinson\u2019s disease of substantia nigra dopamine neurons containing calbindin-D28K","volume":"526","author":"Yamada","year":"1990","journal-title":"Brain Research"},{"key":"bib100","doi-asserted-by":"publisher","first-page":"12413","DOI":"10.1523\/JNEUROSCI.1077-11.2011","type":"journal-article","article-title":"Lmx1a and lmx1b function cooperatively to regulate proliferation, specification, and differentiation of midbrain dopaminergic progenitors","volume":"31","author":"Yan","year":"2011","journal-title":"The Journal of Neuroscience"},{"key":"bib101","doi-asserted-by":"publisher","DOI":"10.1186\/s12974-018-1053-4","type":"journal-article","article-title":"MicroRNA-124 regulates the expression of MEKK3 in the inflammatory pathogenesis of Parkinson\u2019s disease","volume":"15","author":"Yao","year":"2018","journal-title":"Journal of Neuroinflammation"},{"key":"bib102","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/s41586-023-06812-z","type":"journal-article","article-title":"A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain","volume":"624","author":"Yao","year":"2023","journal-title":"Nature"},{"key":"bib103","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.nbd.2015.02.031","type":"journal-article","article-title":"Progressive dopaminergic alterations and mitochondrial abnormalities in LRRK2 G2019S knock-in mice","volume":"78","author":"Yue","year":"2015","journal-title":"Neurobiology of Disease"},{"key":"bib104","type":"software","article-title":"Clustree","volume-title":"Software Heritage","author":"Zappia","year":"2023","unstructured":"Zappia L, Rau A, Lang M, Hoffman P. 2023. Clustree. Software Heritage. swh:1:rev:24900bdf459c29812c716ba9f889c58685f957ed. https:\/\/archive.softwareheritage.org\/swh:1:dir:2bd6bb8451d5cf150a67e009204812e1558c9138;origin=https:\/\/github.com\/lazappi\/clustree;visit=swh:1:snp:64fe40a85ed23f721fac61012a3d7fea5d38a7c4;anchor=swh:1:rev:24900bdf459c29812c716ba9f889c58685f957ed."},{"key":"bib105","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1038\/s41588-022-01167-z","type":"journal-article","article-title":"Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data","volume":"54","author":"Zhang","year":"2022","journal-title":"Nature Genetics"},{"key":"bib106","doi-asserted-by":"publisher","DOI":"10.1016\/j.archger.2021.104588","type":"journal-article","article-title":"Neuroprotective effects of microRNA 124 in Parkinson\u2019s disease mice","volume":"99","author":"Zhang","year":"2022","journal-title":"Archives of Gerontology and Geriatrics"},{"key":"bib107","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/s41586-023-06808-9","type":"journal-article","article-title":"Molecularly defined and spatially resolved cell atlas of the whole mouse brain","volume":"624","author":"Zhang","year":"2023","journal-title":"Nature"},{"key":"bib108","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.201900353","type":"journal-article","article-title":"PISD is a mitochondrial disease gene causing skeletal dysplasia, cataracts, and white matter changes","volume":"2","author":"Zhao","year":"2019","journal-title":"Life Science Alliance"},{"key":"dataset1","type":"dataset","article-title":"Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019S model of Parkinson's disease","volume-title":"NCBI Gene Expression Omnibus","author":"Gaerner","year":"2024","unstructured":"Gaerner Z, Oram C, Schneeweis A, Awatramani R, Poulin J. 2024. Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019S model of Parkinson's disease. NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE271781. GSE271781."},{"key":"dataset2","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.12636327","type":"dataset","article-title":"MERFISH Dataset of Mouse Dopamine Neurons_03Jul2024","volume-title":"Zenodo","author":"Cameron","year":"2024","unstructured":"Cameron O. 2024. MERFISH Dataset of Mouse Dopamine Neurons_03Jul2024. Zenodo."},{"key":"dataset3","type":"dataset","article-title":"Single nucleus RNAseq of midbrain dopaminergic neuronal nuclei isolated by FACS","volume-title":"NCBI Gene Expression Omnibus","author":"Gaertner","year":"2023","unstructured":"Gaertner Z, Azcorra M, Awatramani R, Dombeck DA. 2023. Single nucleus RNAseq of midbrain dopaminergic neuronal nuclei isolated by FACS. NCBI Gene Expression Omnibus. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE222558. GSE222558."}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/101035\/elife-101035-v1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/101035\/elife-101035-v1.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/101035","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:38:56Z","timestamp":1787564336000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/101035"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,12]]},"references-count":111,"alternative-id":["10.7554\/eLife.101035"],"URL":"https:\/\/doi.org\/10.7554\/elife.101035","archive":["CLOCKSS"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.06.06.597807","asserted-by":"subject"}],"references":[{"id-type":"accession","id":"GSE222558","asserted-by":"subject"}],"is-same-as":[{"id-type":"doi","id":"10.7554\/eLife.101035.3","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.7554\/eLife.101035.1","asserted-by":"subject"},{"id-type":"doi","id":"10.7554\/eLife.101035.2","asserted-by":"subject"}],"is-supplemented-by":[{"id-type":"accession","id":"GSE271781","asserted-by":"subject"},{"id-type":"doi","id":"10.5281\/zenodo.12636327","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:acdb8187f0bafd685026137a864bc7ee8f7c70da;origin=https:\/\/github.com\/AwatramaniLab\/Gaertner_Oram_etal;visit=swh:1:snp:9ffbc4187c0915f4adabbe0dcfa34dd7e374ec66;anchor=swh:1:rev:cc4374e0b87b121d2117707467cd79a80e0bb44d","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/archive.softwareheritage.org\/swh:1:dir:2bd6bb8451d5cf150a67e009204812e1558c9138;origin=https:\/\/github.com\/lazappi\/clustree;visit=swh:1:snp:64fe40a85ed23f721fac61012a3d7fea5d38a7c4;anchor=swh:1:rev:24900bdf459c29812c716ba9f889c58685f957ed","asserted-by":"subject"}]},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,12]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"RP101035"}}