{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,31]],"date-time":"2026-10-31T00:46:16Z","timestamp":1793407576963,"version":"4.5.0"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T00:00:00Z","timestamp":1711497600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T00:00:00Z","timestamp":1711497600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100010661","name":"EC | Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["810287"],"award-info":[{"award-number":["810287"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Ministry of Economy and Competitiveness | Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI19\/01772"],"award-info":[{"award-number":["PI19\/01772"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Ministry of Economy and Competitiveness | Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["IHMC22\/00027"],"award-info":[{"award-number":["IHMC22\/00027"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Data"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Despite the wealth of publicly available single-cell datasets, our understanding of distinct resident immune cells and their unique features in diverse human organs remains limited. To address this, we compiled a meta-analysis dataset of 114,275\n                    <jats:italic>CD45<\/jats:italic>\n                    + immune cells sourced from 14 organs in healthy donors. While the transcriptome of immune cells remains relatively consistent across organs, our analysis has unveiled organ-specific gene expression differences (\n                    <jats:italic>GTPX3<\/jats:italic>\n                    in kidney,\n                    <jats:italic>DNTT<\/jats:italic>\n                    and\n                    <jats:italic>ACVR2B<\/jats:italic>\n                    in thymus). These alterations are linked to different transcriptional factor activities and pathways including metabolism.\n                    <jats:italic>TNF-\u03b1<\/jats:italic>\n                    signaling through the\n                    <jats:italic>NFkB<\/jats:italic>\n                    pathway was found in several organs and immune compartments. The presence of distinct expression profiles for\n                    <jats:italic>NFkB<\/jats:italic>\n                    family genes and their target genes, including cytokines, underscores their pivotal role in cell positioning. Taken together, immune cells serve a dual role: safeguarding the organs and dynamically adjusting to the intricacies of the host organ environment, thereby actively contributing to its functionality and overall homeostasis.\n                  <\/jats:p>","DOI":"10.1038\/s41597-024-03152-z","type":"journal-article","created":{"date-parts":[[2024,3,27]],"date-time":"2024-03-27T10:01:54Z","timestamp":1711533714000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1653-0327","authenticated-orcid":false,"given":"Maria","family":"Tsagiopoulou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonal","family":"Rashmi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergio","family":"Aguilar-Fernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Nieto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7219-632X","authenticated-orcid":false,"given":"Ivo G.","family":"Gut","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,27]]},"reference":[{"key":"3152_CR1","doi-asserted-by":"crossref","unstructured":"Pappalardo, J.L. et al. Transcriptomic and clonal characterization of T cells in the human central nervous system. Sci Immunol 5 (2020).","DOI":"10.1126\/sciimmunol.abb8786"},{"key":"3152_CR2","doi-asserted-by":"publisher","first-page":"1615","DOI":"10.1016\/j.jaci.2020.01.042","volume":"145","author":"H He","year":"2020","unstructured":"He, H. et al. Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis. J Allergy Clin Immunol 145, 1615\u20131628 (2020).","journal-title":"J Allergy Clin Immunol"},{"key":"3152_CR3","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1016\/j.tig.2021.03.007","volume":"37","author":"RGH Lindeboom","year":"2021","unstructured":"Lindeboom, R. G. H., Regev, A. & Teichmann, S. A. Towards a Human Cell Atlas: Taking Notes from the Past. Trends Genet 37, 625\u2013630 (2021).","journal-title":"Trends Genet"},{"key":"3152_CR4","doi-asserted-by":"publisher","first-page":"1913","DOI":"10.1101\/gr.273300.120","volume":"31","author":"P Nieto","year":"2021","unstructured":"Nieto, P. et al. A single-cell tumor immune atlas for precision oncology. Genome Res 31, 1913\u20131926 (2021).","journal-title":"Genome Res"},{"key":"3152_CR5","doi-asserted-by":"publisher","first-page":"eabl5197","DOI":"10.1126\/science.abl5197","volume":"376","author":"C Dominguez Conde","year":"2022","unstructured":"Dominguez Conde, C. et al. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 376, eabl5197 (2022).","journal-title":"Science"},{"key":"3152_CR6","doi-asserted-by":"publisher","DOI":"10.1126\/science.abo0510","volume":"376","author":"C Suo","year":"2022","unstructured":"Suo, C. et al. Mapping the developing human immune system across organs. Science 376, eabo0510 (2022).","journal-title":"Science"},{"key":"3152_CR7","doi-asserted-by":"publisher","DOI":"10.1126\/science.abl4290","volume":"376","author":"G Eraslan","year":"2022","unstructured":"Eraslan, G. et al. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science 376, eabl4290 (2022).","journal-title":"Science"},{"key":"3152_CR8","doi-asserted-by":"publisher","first-page":"eabl4896","DOI":"10.1126\/science.abl4896","volume":"376","author":"C Tabula Sapiens","year":"2022","unstructured":"Tabula Sapiens, C. et al. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science 376, eabl4896 (2022).","journal-title":"Science"},{"key":"3152_CR9","unstructured":"Massoni-Badosa, R. et al. An Atlas of Cells in the Human Tonsil. bioRxiv, 2022.2006.2024.497299 (2022)."},{"key":"3152_CR10","doi-asserted-by":"publisher","first-page":"2657","DOI":"10.1007\/s00018-015-1895-1","volume":"72","author":"J Perera","year":"2015","unstructured":"Perera, J. & Huang, H. The development and function of thymic B cells. Cell Mol Life Sci 72, 2657\u20132663 (2015).","journal-title":"Cell Mol Life Sci"},{"key":"3152_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-019-0351-8","volume":"7","author":"J Liao","year":"2020","unstructured":"Liao, J. et al. Single-cell RNA sequencing of human kidney. Sci Data 7, 4 (2020).","journal-title":"Sci Data"},{"key":"3152_CR12","doi-asserted-by":"publisher","first-page":"1461","DOI":"10.1126\/science.aat5031","volume":"365","author":"BJ Stewart","year":"2019","unstructured":"Stewart, B. J. et al. Spatiotemporal immune zonation of the human kidney. Science 365, 1461\u20131466 (2019).","journal-title":"Science"},{"key":"3152_CR13","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/s41586-023-05769-3","volume":"619","author":"BB Lake","year":"2023","unstructured":"Lake, B. B. et al. An atlas of healthy and injured cell states and niches in the human kidney. Nature 619, 585\u2013594 (2023).","journal-title":"Nature"},{"key":"3152_CR14","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1016\/j.celrep.2018.01.015","volume":"22","author":"S Cepeda","year":"2018","unstructured":"Cepeda, S. et al. Age-Associated Decline in Thymic B Cell Expression of Aire and Aire-Dependent Self-Antigens. Cell Rep 22, 1276\u20131287 (2018).","journal-title":"Cell Rep"},{"key":"3152_CR15","doi-asserted-by":"publisher","first-page":"3322","DOI":"10.1073\/pnas.0511299103","volume":"103","author":"F Weerkamp","year":"2006","unstructured":"Weerkamp, F. et al. Wnt signaling in the thymus is regulated by differential expression of intracellular signaling molecules. Proc Natl Acad Sci USA 103, 3322\u20133326 (2006).","journal-title":"Proc Natl Acad Sci USA"},{"key":"3152_CR16","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1111\/cei.13269","volume":"196","author":"S Heidt","year":"2019","unstructured":"Heidt, S. et al. Presence of intragraft B cells during acute renal allograft rejection is accompanied by changes in peripheral blood B cell subsets. Clin Exp Immunol 196, 403\u2013414 (2019).","journal-title":"Clin Exp Immunol"},{"key":"3152_CR17","doi-asserted-by":"publisher","first-page":"a000182","DOI":"10.1101\/cshperspect.a000182","volume":"2","author":"S Gerondakis","year":"2010","unstructured":"Gerondakis, S. & Siebenlist, U. Roles of the NF-kappaB pathway in lymphocyte development and function. Cold Spring Harb Perspect Biol 2, a000182 (2010).","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"3152_CR18","doi-asserted-by":"crossref","unstructured":"Sokol, C.L. & Luster, A.D. The chemokine system in innate immunity. Cold Spring Harb Perspect Biol 7 (2015).","DOI":"10.1101\/cshperspect.a016303"},{"key":"3152_CR19","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1146\/annurev-immunol-032713-120145","volume":"32","author":"JW Griffith","year":"2014","unstructured":"Griffith, J. W., Sokol, C. L. & Luster, A. D. Chemokines and chemokine receptors: positioning cells for host defense and immunity. Annu Rev Immunol 32, 659\u2013702 (2014).","journal-title":"Annu Rev Immunol"},{"key":"3152_CR20","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/s41421-020-0157-z","volume":"6","author":"J Zhao","year":"2020","unstructured":"Zhao, J. et al. Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell Discov 6, 22 (2020).","journal-title":"Cell Discov"},{"key":"3152_CR21","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1111\/j.1600-065X.2007.00565.x","volume":"220","author":"YY Wan","year":"2007","unstructured":"Wan, Y. Y. & Flavell, R. A. \u2018Yin-Yang\u2019 functions of transforming growth factor-beta and T regulatory cells in immune regulation. Immunol Rev 220, 199\u2013213 (2007).","journal-title":"Immunol Rev"},{"key":"3152_CR22","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1038\/nature13989","volume":"518","author":"E Gomez Perdiguero","year":"2015","unstructured":"Gomez Perdiguero, E. et al. Tissue-resident macrophages originate from yolk-sac-derived erythro-myeloid progenitors. Nature 518, 547\u2013551 (2015).","journal-title":"Nature"},{"key":"3152_CR23","doi-asserted-by":"publisher","first-page":"eadd7564","DOI":"10.1126\/science.add7564","volume":"381","author":"I Goh","year":"2023","unstructured":"Goh, I. et al. Yolk sac cell atlas reveals multiorgan functions during human early development. Science 381, eadd7564 (2023).","journal-title":"Science"},{"key":"3152_CR24","doi-asserted-by":"publisher","first-page":"e0223264","DOI":"10.1371\/journal.pone.0223264","volume":"14","author":"CW Bruggeman","year":"2019","unstructured":"Bruggeman, C. W. et al. Tissue-specific expression of IgG receptors by human macrophages ex vivo. PLoS One 14, e0223264 (2019).","journal-title":"PLoS One"},{"key":"3152_CR25","doi-asserted-by":"publisher","first-page":"e0204108","DOI":"10.1371\/journal.pone.0204108","volume":"13","author":"T Fuchs","year":"2018","unstructured":"Fuchs, T. et al. Expression of combinatorial immunoglobulins in macrophages in the tumor microenvironment. PLoS One 13, e0204108 (2018).","journal-title":"PLoS One"},{"key":"3152_CR26","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-37511-9","volume":"9","author":"K Iio","year":"2019","unstructured":"Iio, K. et al. Parathyroid hormone and premature thymus ageing in patients with chronic kidney disease. Sci Rep 9, 813 (2019).","journal-title":"Sci Rep"},{"key":"3152_CR27","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/s12979-020-00175-z","volume":"17","author":"MGH Betjes","year":"2020","unstructured":"Betjes, M. G. H., Langerak, A. W., Klepper, M. & Litjens, N. H. R. A very low thymus function identifies patients with substantial increased risk for long-term mortality after kidney transplantation. Immun Ageing 17, 4 (2020).","journal-title":"Immun Ageing"},{"key":"3152_CR28","doi-asserted-by":"publisher","first-page":"2090","DOI":"10.1093\/ckj\/sfaa276","volume":"14","author":"A Takahashi","year":"2021","unstructured":"Takahashi, A. et al. The histopathological spectrum of kidney biopsies in patients with thymoma and myasthenia gravis: a report of 24 biopsies from a single institution. Clin Kidney J 14, 2090\u20132100 (2021).","journal-title":"Clin Kidney J"},{"key":"3152_CR29","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.766698","volume":"12","author":"J Castaneda","year":"2021","unstructured":"Castaneda, J. et al. The Multifaceted Roles of B Cells in the Thymus: From Immune Tolerance to Autoimmunity. Front Immunol 12, 766698 (2021).","journal-title":"Front Immunol"},{"key":"3152_CR30","doi-asserted-by":"publisher","first-page":"102314","DOI":"10.1016\/j.jaut.2019.102314","volume":"104","author":"I Morianos","year":"2019","unstructured":"Morianos, I., Papadopoulou, G., Semitekolou, M. & Xanthou, G. Activin-A in the regulation of immunity in health and disease. J Autoimmun 104, 102314 (2019).","journal-title":"J Autoimmun"},{"key":"3152_CR31","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.4049\/jimmunol.164.4.1829","volume":"164","author":"C Moratz","year":"2000","unstructured":"Moratz, C. et al. Regulator of G protein signaling 1 (RGS1) markedly impairs Gi alpha signaling responses of B lymphocytes. J Immunol 164, 1829\u20131838 (2000).","journal-title":"J Immunol"},{"key":"3152_CR32","doi-asserted-by":"publisher","first-page":"G32","DOI":"10.1152\/ajpgi.00064.2011","volume":"301","author":"RF Burk","year":"2011","unstructured":"Burk, R. F., Olson, G. E., Winfrey, V. P., Hill, K. E. & Yin, D. Glutathione peroxidase-3 produced by the kidney binds to a population of basement membranes in the gastrointestinal tract and in other tissues. Am J Physiol Gastrointest Liver Physiol 301, G32\u201338 (2011).","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"3152_CR33","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/s12876-018-0752-8","volume":"18","author":"S Oltedal","year":"2018","unstructured":"Oltedal, S. et al. Expression profiling and intracellular localization studies of the novel Proline-, Histidine-, and Glycine-rich protein 1 suggest an essential role in gastro-intestinal epithelium and a potential clinical application in colorectal cancer diagnostics. BMC Gastroenterol 18, 26 (2018).","journal-title":"BMC Gastroenterol"},{"key":"3152_CR34","doi-asserted-by":"publisher","first-page":"1292","DOI":"10.1002\/eji.1830270534","volume":"27","author":"MW Schilham","year":"1997","unstructured":"Schilham, M. W., Moerer, P., Cumano, A. & Clevers, H. C. Sox-4 facilitates thymocyte differentiation. Eur J Immunol 27, 1292\u20131295 (1997).","journal-title":"Eur J Immunol"},{"key":"3152_CR35","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/ni.3005","volume":"15","author":"C Schneider","year":"2014","unstructured":"Schneider, C. et al. Induction of the nuclear receptor PPAR-gamma by the cytokine GM-CSF is critical for the differentiation of fetal monocytes into alveolar macrophages. Nat Immunol 15, 1026\u20131037 (2014).","journal-title":"Nat Immunol"},{"key":"3152_CR36","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1146\/annurev-immunol-032712-100024","volume":"32","author":"EV Rothenberg","year":"2014","unstructured":"Rothenberg, E. V. Transcriptional control of early T and B cell developmental choices. Annu Rev Immunol 32, 283\u2013321 (2014).","journal-title":"Annu Rev Immunol"},{"key":"3152_CR37","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.smim.2005.01.003","volume":"17","author":"RC Su","year":"2005","unstructured":"Su, R. C., Sridharan, R. & Smale, S. T. Assembly of silent chromatin during thymocyte development. Semin Immunol 17, 129\u2013140 (2005).","journal-title":"Semin Immunol"},{"key":"3152_CR38","doi-asserted-by":"publisher","first-page":"2833","DOI":"10.1681\/ASN.2020060806","volume":"31","author":"BR Conway","year":"2020","unstructured":"Conway, B. R. et al. Kidney Single-Cell Atlas Reveals Myeloid Heterogeneity in Progression and Regression of Kidney Disease. J Am Soc Nephrol 31, 2833\u20132854 (2020).","journal-title":"J Am Soc Nephrol"},{"key":"3152_CR39","doi-asserted-by":"publisher","first-page":"6418","DOI":"10.1038\/sj.onc.1208794","volume":"24","author":"B Lucas","year":"2005","unstructured":"Lucas, B. et al. HNF4alpha reduces proliferation of kidney cells and affects genes deregulated in renal cell carcinoma. Oncogene 24, 6418\u20136431 (2005).","journal-title":"Oncogene"},{"key":"3152_CR40","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1038\/s41590-019-0407-0","volume":"20","author":"G Caputa","year":"2019","unstructured":"Caputa, G., Castoldi, A. & Pearce, E. J. Metabolic adaptations of tissue-resident immune cells. Nat Immunol 20, 793\u2013801 (2019).","journal-title":"Nat Immunol"},{"key":"3152_CR41","doi-asserted-by":"publisher","first-page":"a001651","DOI":"10.1101\/cshperspect.a001651","volume":"1","author":"T Lawrence","year":"2009","unstructured":"Lawrence, T. The nuclear factor NF-kappaB pathway in inflammation. Cold Spring Harb Perspect Biol 1, a001651 (2009).","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"3152_CR42","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abn6240","volume":"8","author":"M Son","year":"2022","unstructured":"Son, M. et al. Spatiotemporal NF-kappaB dynamics encodes the position, amplitude, and duration of local immune inputs. Sci Adv 8, eabn6240 (2022).","journal-title":"Sci Adv"},{"key":"3152_CR43","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1016\/j.immuni.2015.03.003","volume":"42","author":"M Baratin","year":"2015","unstructured":"Baratin, M. et al. Homeostatic NF-kappaB Signaling in Steady-State Migratory Dendritic Cells Regulates Immune Homeostasis and Tolerance. Immunity 42, 627\u2013639 (2015).","journal-title":"Immunity"},{"key":"3152_CR44","doi-asserted-by":"publisher","first-page":"E846","DOI":"10.1073\/pnas.1319397111","volume":"111","author":"A Silva","year":"2014","unstructured":"Silva, A., Cornish, G., Ley, S. C. & Seddon, B. NF-kappaB signaling mediates homeostatic maturation of new T cells. Proc Natl Acad Sci USA 111, E846\u2013855 (2014).","journal-title":"Proc Natl Acad Sci USA"},{"key":"3152_CR45","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40107-1","volume":"14","author":"CJ Pritzl","year":"2023","unstructured":"Pritzl, C. J. et al. IKK2\/NFkB signaling controls lung resident CD8(+) T cell memory during influenza infection. Nat Commun 14, 4331 (2023).","journal-title":"Nat Commun"},{"key":"3152_CR46","doi-asserted-by":"publisher","first-page":"7099","DOI":"10.1002\/j.1460-2075.1996.tb01101.x","volume":"15","author":"G Grigoriadis","year":"1996","unstructured":"Grigoriadis, G. et al. The Rel subunit of NF-kappaB-like transcription factors is a positive and negative regulator of macrophage gene expression: distinct roles for Rel in different macrophage populations. EMBO J 15, 7099\u20137107 (1996).","journal-title":"EMBO J"},{"key":"3152_CR47","doi-asserted-by":"publisher","first-page":"3530","DOI":"10.1016\/j.celrep.2018.11.086","volume":"25","author":"GH Henry","year":"2018","unstructured":"Henry, G. H. et al. A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. Cell Rep 25, 3530\u20133542 e3535 (2018).","journal-title":"Cell Rep"},{"key":"3152_CR48","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2018100811","volume":"38","author":"SW Lukowski","year":"2019","unstructured":"Lukowski, S. W. et al. A single-cell transcriptome atlas of the adult human retina. EMBO J 38, e100811 (2019).","journal-title":"EMBO J"},{"key":"3152_CR49","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1038\/s41586-020-2797-4","volume":"588","author":"M Litvinukova","year":"2020","unstructured":"Litvinukova, M. et al. Cells of the adult human heart. Nature 588, 466\u2013472 (2020).","journal-title":"Nature"},{"key":"3152_CR50","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-57110-6","volume":"10","author":"AB Rubenstein","year":"2020","unstructured":"Rubenstein, A. B. et al. Single-cell transcriptional profiles in human skeletal muscle. Sci Rep 10, 229 (2020).","journal-title":"Sci Rep"},{"key":"3152_CR51","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-17876-0","volume":"11","author":"D Agarwal","year":"2020","unstructured":"Agarwal, D. et al. A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders. Nat Commun 11, 4183 (2020).","journal-title":"Nat Commun"},{"key":"3152_CR52","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1038\/s41586-019-0992-y","volume":"567","author":"K Parikh","year":"2019","unstructured":"Parikh, K. et al. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature 567, 49\u201355 (2019).","journal-title":"Nature"},{"key":"3152_CR53","unstructured":"Park, J.E. et al. A cell atlas of human thymic development defines T cell repertoire formation. Science 367 (2020)."},{"key":"3152_CR54","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","volume":"177","author":"T Stuart","year":"2019","unstructured":"Stuart, T. et al. Comprehensive Integration of Single-Cell Data. Cell 177, 1888\u20131902 e1821 (2019).","journal-title":"Cell"},{"key":"3152_CR55","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 16, 1289\u20131296 (2019).","journal-title":"Nat Methods"},{"key":"3152_CR56","doi-asserted-by":"publisher","first-page":"3796","DOI":"10.1016\/j.csbj.2021.06.043","volume":"19","author":"M Andreatta","year":"2021","unstructured":"Andreatta, M. & Carmona, S. J. UCell: Robust and scalable single-cell gene signature scoring. Comput Struct Biotechnol J 19, 3796\u20133798 (2021).","journal-title":"Comput Struct Biotechnol J"},{"key":"3152_CR57","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu, G., Wang, L. G., Han, Y. & He, Q. Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284\u2013287 (2012).","journal-title":"OMICS"},{"key":"3152_CR58","doi-asserted-by":"publisher","first-page":"1436","DOI":"10.1016\/j.celrep.2018.10.045","volume":"25","author":"S Suo","year":"2018","unstructured":"Suo, S. et al. Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas. Cell Rep 25, 1436\u20131445 e1433 (2018).","journal-title":"Cell Rep"},{"key":"3152_CR59","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.10197112","author":"M Tsagiopoulou","year":"2024","unstructured":"Tsagiopoulou, M. Multi-organ CD45+ immune cell atlas. Zenodo. https:\/\/doi.org\/10.5281\/zenodo.10197112 (2024)."},{"key":"3152_CR60","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.10469288","author":"MariaTsayo","year":"2024","unstructured":"MariaTsayo. MariaTsayo\/mulTI_Metatlas: Zenodo_v2. Zenodo. https:\/\/doi.org\/10.5281\/zenodo.10469288 (2024)."}],"container-title":["Scientific Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41597-024-03152-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-024-03152-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-024-03152-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,30]],"date-time":"2024-03-30T13:04:37Z","timestamp":1711803877000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41597-024-03152-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,27]]},"references-count":60,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["3152"],"URL":"https:\/\/doi.org\/10.1038\/s41597-024-03152-z","relation":{"references":[{"id-type":"doi","id":"10.5281\/zenodo.10197112","asserted-by":"subject"},{"id-type":"doi","id":"10.5281\/zenodo.10469288","asserted-by":"subject"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.05.29.542692","asserted-by":"object"}]},"ISSN":["2052-4463"],"issn-type":[{"value":"2052-4463","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,27]]},"assertion":[{"value":"27 June 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 March 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 March 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"316"}}