{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T16:49:58Z","timestamp":1782838198976,"version":"3.54.5"},"reference-count":27,"publisher":"The Company of Biologists","issue":"10","license":[{"start":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T00:00:00Z","timestamp":1697673600000},"content-version":"vor","delay-in-days":4,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"crossref","award":["BMBF 01GQ1405"],"award-info":[{"award-number":["BMBF 01GQ1405"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["D.721090\/20.001"],"award-info":[{"award-number":["D.721090\/20.001"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Chica and Heinz Schaller Foundation"},{"name":"Deutsches Krebsforschungszentrum"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>The developing brain has a well-organized anatomical structure comprising different types of neural and non-neural cells. Stem cells, progenitors and newborn neurons tightly interact with their neighbouring cells and tissue microenvironment, and this intricate interplay ultimately shapes the output of neurogenesis. Given the relevance of spatial cues during brain development, we acknowledge the necessity for a spatial transcriptomics map accessible to the neurodevelopmental community. To fulfil this need, we generated spatially resolved RNA sequencing (RNAseq) data from embryonic day 13.5 mouse brain sections immunostained for mitotic active neural and vascular cells. Unsupervised clustering defined specific cell type populations of diverse lineages and differentiation states. Differential expression analysis revealed unique transcriptional signatures across specific brain areas, uncovering novel features inherent to particular anatomical domains. Finally, we integrated existing single-cell RNAseq datasets into our spatial transcriptomics map, adding tissue context to single-cell RNAseq data. In summary, we provide a valuable tool that enables the exploration and discovery of unforeseen molecular players involved in neurogenesis, particularly in the crosstalk between different cell types.<\/jats:p>","DOI":"10.1242\/bio.060151","type":"journal-article","created":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T07:02:08Z","timestamp":1697698928000},"source":"Crossref","is-referenced-by-count":6,"title":["Spatial transcriptomics map of the embryonic mouse brain \u2013 a tool to explore neurogenesis"],"prefix":"10.1242","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1751-7455","authenticated-orcid":false,"given":"Barbara","family":"Di Marco","sequence":"first","affiliation":[{"name":"the German Cancer Research Center (DKFZ) and the Medical Faculty of the Heidelberg University 1 Department of Clinical Neurobiology at , Im Neuenheimer Feld 280, 69120 Heidelberg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Javier","family":"V\u00e1zquez-Mar\u00edn","sequence":"additional","affiliation":[{"name":"Center for Organismal Studies, Heidelberg University 2 , Im Neuenheimer Feld 230, Heidelberg 69120 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Monyer","sequence":"additional","affiliation":[{"name":"the German Cancer Research Center (DKFZ) and the Medical Faculty of the Heidelberg University 1 Department of Clinical Neurobiology at , Im Neuenheimer Feld 280, 69120 Heidelberg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3889-4524","authenticated-orcid":false,"given":"L\u00e1zaro","family":"Centanin","sequence":"additional","affiliation":[{"name":"Center for Organismal Studies, Heidelberg University 2 , Im Neuenheimer Feld 230, Heidelberg 69120 , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5063-3653","authenticated-orcid":false,"given":"Julieta","family":"Alfonso","sequence":"additional","affiliation":[{"name":"the German Cancer Research Center (DKFZ) and the Medical Faculty of the Heidelberg University 1 Department of Clinical Neurobiology at , Im Neuenheimer Feld 280, 69120 Heidelberg , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2023,10,19]]},"reference":[{"key":"2023101911012938900_BIO060151C1","doi-asserted-by":"publisher","first-page":"45656","DOI":"10.1038\/srep45656","article-title":"Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types","volume":"7","author":"Chen","year":"2017","journal-title":"Sci. Rep."},{"key":"2023101911012938900_BIO060151C2","doi-asserted-by":"publisher","first-page":"799","DOI":"10.16288\/j.yczz.20-080","article-title":"CNGBdb: China National GeneBank DataBase","volume":"42","author":"Chen","year":"2020","journal-title":"Yi Chuan"},{"key":"2023101911012938900_BIO060151C3","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1016\/j.cell.2020.06.038","article-title":"Spatial transcriptomics and in situ sequencing to study Alzheimer's disease","volume":"182","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"2023101911012938900_BIO060151C4","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"2023101911012938900_BIO060151C5","doi-asserted-by":"publisher","first-page":"108256","DOI":"10.1016\/j.celrep.2020.108256","article-title":"Reciprocal interaction between vascular filopodia and neural stem cells shapes neurogenesis in the ventral telencephalon","volume":"33","author":"Di Marco","year":"2020","journal-title":"Cell Rep."},{"key":"2023101911012938900_BIO060151C6","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat. Protoc."},{"key":"2023101911012938900_BIO060151C7","doi-asserted-by":"publisher","first-page":"1644","DOI":"10.1016\/j.cell.2015.05.041","article-title":"Embryonic origin of postnatal neural stem cells","volume":"161","author":"Fuentealba","year":"2015","journal-title":"Cell"},{"key":"2023101911012938900_BIO060151C8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2183\/pjab.92.1","article-title":"From migration to settlement: the pathways, migration modes and dynamics of neurons in the developing brain","volume":"92","author":"Hatanaka","year":"2016","journal-title":"Proc. Jpn. Acad. Ser. B Phys. Biol. Sci."},{"key":"2023101911012938900_BIO060151C9","doi-asserted-by":"publisher","first-page":"3196","DOI":"10.1073\/pnas.0308600100","article-title":"Neurons arise in the basal neuroepithelium of the early mammalian telencephalon: a major site of neurogenesis","volume":"101","author":"Haubensak","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023101911012938900_BIO060151C10","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"2023101911012938900_BIO060151C11","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/s41586-021-03775-x","article-title":"Molecular architecture of the developing mouse brain","volume":"596","author":"La Manno","year":"2021","journal-title":"Nature"},{"key":"2023101911012938900_BIO060151C12","doi-asserted-by":"publisher","first-page":"924","DOI":"10.15252\/embj.201592372","article-title":"Relief of hypoxia by angiogenesis promotes neural stem cell differentiation by targeting glycolysis","volume":"35","author":"Lange","year":"2016","journal-title":"EMBO J."},{"key":"2023101911012938900_BIO060151C13","doi-asserted-by":"publisher","first-page":"11802","DOI":"10.1073\/pnas.0805180105","article-title":"The role of ATP signaling in the migration of intermediate neuronal progenitors to the neocortical subventricular zone","volume":"105","author":"Liu","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023101911012938900_BIO060151C14","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2020.10.026","article-title":"High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue","volume":"183","author":"Liu","year":"2020","journal-title":"Cell"},{"key":"2023101911012938900_BIO060151C15","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.conb.2014.01.015","article-title":"Lineage origins of GABAergic versus glutamatergic neurons in the neocortex","volume":"26","author":"Mar\u00edn","year":"2014","journal-title":"Curr. Opin. Neurobiol."},{"key":"2023101911012938900_BIO060151C16","doi-asserted-by":"publisher","first-page":"a001834","DOI":"10.1101\/cshperspect.a001834","article-title":"Guiding neuronal cell migrations","volume":"2","author":"Mar\u00edn","year":"2010","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2023101911012938900_BIO060151C17","doi-asserted-by":"publisher","first-page":"dev197962","DOI":"10.1242\/DEV.197962","article-title":"Single-cell transcriptomics of the early developing mouse cerebral cortex disentangle the spatial and temporal components of neuronal fate acquisition","volume":"148","author":"Moreau","year":"2021","journal-title":"Development"},{"key":"2023101911012938900_BIO060151C18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1113\/jphysiol.2003.045062","article-title":"Synaptogenesis in the CNS: an odyssey from wiring together to firing together","volume":"552","author":"Munno","year":"2003","journal-title":"J. Physiol."},{"key":"2023101911012938900_BIO060151C19","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1038\/nn1172","article-title":"Cortical neurons arise in symmetric and asymmetric division zones and migrate through specific phases","volume":"7","author":"Noctor","year":"2004","journal-title":"Nat. Neurosci."},{"key":"2023101911012938900_BIO060151C20","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1523\/JNEUROSCI.23-01-00167.2003","article-title":"Identification of two distinct progenitor populations in the lateral ganglionic eminence: implications for striatal and olfactory bulb neurogenesis","volume":"23","author":"Stenman","year":"2002","journal-title":"J. Neurosci."},{"key":"2023101911012938900_BIO060151C21","doi-asserted-by":"publisher","first-page":"baaa073","DOI":"10.1093\/DATABASE\/BAAA073","article-title":"A curated database reveals trends in single-cell transcriptomics","volume":"2020","author":"Svensson","year":"2020","journal-title":"Database"},{"key":"2023101911012938900_BIO060151C22","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1523\/JNEUROSCI.13-02-00820.1993","article-title":"Cell cycle parameters and patterns of nuclear movement in the neocortical proliferative zone of the fetal mouse","volume":"13","author":"Takahashi","year":"1993","journal-title":"J. Neurosci."},{"key":"2023101911012938900_BIO060151C23","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1016\/j.devcel.2016.02.023","article-title":"Vascular influence on ventral telencephalic progenitors and neocortical interneuron production","volume":"36","author":"Tan","year":"2016","journal-title":"Dev. Cell"},{"key":"2023101911012938900_BIO060151C24","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1146\/annurev-cellbio-101011-155801","article-title":"The cell biology of neurogenesis: toward an understanding of the development and evolution of the neocortex","volume":"30","author":"Taverna","year":"2014","journal-title":"Annu. Rev. Cell Dev. Biol."},{"key":"2023101911012938900_BIO060151C25","doi-asserted-by":"publisher","first-page":"3942","DOI":"10.1002\/1873-3468.12829","article-title":"Radial glia in the ventral telencephalon","volume":"591","author":"Turrero Garc\u00eda","year":"2017","journal-title":"FEBS Lett."},{"key":"2023101911012938900_BIO060151C26","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/s41586-018-0698-6","article-title":"Single-cell reconstruction of the early maternal\u2013fetal interface in humans","volume":"563","author":"Vento-Tormo","year":"2018","journal-title":"Nature"},{"key":"2023101911012938900_BIO060151C27","doi-asserted-by":"publisher","DOI":"10.1101\/2022.03.11.481421","article-title":"STOmicsDB: a database of spatial transcriptomic data","author":"Xu","year":"2022","journal-title":"bioRxiv"}],"container-title":["Biology Open"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.logists.com\/bio\/bio\/article-pdf\/doi\/10.1242\/bio.060151\/3234669\/bio060151.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/journals.logists.com\/bio\/bio\/article-pdf\/doi\/10.1242\/bio.060151\/3234669\/bio060151.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,19]],"date-time":"2023-10-19T07:02:17Z","timestamp":1697698937000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.biologists.com\/bio\/article\/12\/10\/bio060151\/333682\/Spatial-transcriptomics-map-of-the-embryonic-mouse"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,15]]},"references-count":27,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2023,10,15]]}},"URL":"https:\/\/doi.org\/10.1242\/bio.060151","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.08.10.552773","asserted-by":"object"}]},"ISSN":["2046-6390"],"issn-type":[{"value":"2046-6390","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,15]]},"article-number":"bio060151"}}