{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:37:06Z","timestamp":1785418626321,"version":"3.56.0"},"posted":{"date-parts":[[2026,6,11]]},"group-title":"Neuroscience","reference-count":83,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,6,11]],"date-time":"2026-06-11T00:00:00Z","timestamp":1781136000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"crossref","award":["U19MH114830"],"award-info":[{"award-number":["U19MH114830"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"crossref"}]},{"award":["1R01NS142815"],"award-info":[{"award-number":["1R01NS142815"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005984","name":"Dr. Miriam and Sheldon G. Adelson Medical Research Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100005984","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100008191","name":"Wings for Life Research Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008191","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100005191","name":"Craig H. Neilsen Foundation","doi-asserted-by":"crossref","award":["SCIRTS Postdoctoral Fellowship"],"award-info":[{"award-number":["SCIRTS Postdoctoral Fellowship"]}],"id":[{"id":"10.13039\/100005191","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,6,11]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                <jats:p>\n                  Understanding how cell types are organized across the central nervous system (CNS) is key to uncovering neural function. Here, we integrate single-nucleus Multiome (RNA+ATAC) sequencing, spatial transcriptomics, and computational analyses to map conserved cell type signatures in the adult mouse brainstem and spinal cord. We identify a shared core of neuronal and non-neuronal cell types, alongside region-specific specializations reflecting distinct functions. Spatial data reveal conserved cellular niches across the brainstem\u2013spinal cord boundary, indicating a continuous organizational logic. Cross-region comparisons uncover recurrent gene expression modules and signaling programs that may support shared circuit features. Chromatin accessibility profiling highlights cell-type-specific regulatory programs and implicates\n                  <jats:italic>Hox<\/jats:italic>\n                  transcription factors in positional identity. Notably, cell-type and positional identities are largely orthogonal, with varying regional influence across neuronal classes: motor neurons show strong positional coupling, whereas glutamatergic and GABAergic interneurons show minimal entrainment. This work provides a reference for the shared molecular architecture of these CNS regions.\n                <\/jats:p>","DOI":"10.64898\/2026.06.09.728039","type":"posted-content","created":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T01:05:12Z","timestamp":1781226312000},"source":"Crossref","is-referenced-by-count":0,"title":["Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6365-7646","authenticated-orcid":false,"given":"Yuan","family":"Gao","sequence":"first","affiliation":[{"name":"Allen Institute, Brain Science, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2638-0454","authenticated-orcid":false,"given":"Evgenii","family":"Kegeles","sequence":"additional","affiliation":[{"name":"F.M. Kirby Neurobiology Center, Boston Children\u2019s Hospital, Boston, MA, USA"},{"name":"Department of Neurology and Ophthalmology, Harvard Medical School, Boston, MA, USA"},{"name":"PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8959-4268","authenticated-orcid":false,"given":"Jingyi","family":"Xie","sequence":"additional","affiliation":[{"name":"Allen Institute, Brain Science, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6146-0404","authenticated-orcid":false,"given":"Changkyu","family":"Lee","sequence":"additional","affiliation":[{"name":"Allen Institute, Brain Science, Seattle, WA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5941-170X","authenticated-orcid":false,"given":"Yunfan","family":"Kong","sequence":"additional","affiliation":[{"name":"F.M. 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