{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T12:19:14Z","timestamp":1784809154092,"version":"3.55.0"},"reference-count":49,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,8,29]],"date-time":"2023-08-29T00:00:00Z","timestamp":1693267200000},"content-version":"vor","delay-in-days":89,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["SFB873"],"award-info":[{"award-number":["SFB873"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cells & Development"],"published-print":{"date-parts":[[2023,6]]},"DOI":"10.1016\/j.cdev.2023.203847","type":"journal-article","created":{"date-parts":[[2023,5,3]],"date-time":"2023-05-03T20:02:45Z","timestamp":1683144165000},"page":"203847","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":9,"special_numbering":"C","title":["Single-cell RNA sequencing of mouse lower respiratory tract epithelial cells: A meta-analysis"],"prefix":"10.1016","volume":"174","author":[{"given":"Leila R.","family":"Martins","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanno","family":"Glimm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Scholl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"7835","key":"10.1016\/j.cdev.2023.203847_bb0005","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1038\/s41586-020-2922-4","article-title":"A molecular cell atlas of the human lung from single-cell RNA sequencing","volume":"587","author":"Travaglini","year":"2020","journal-title":"Nature"},{"issue":"7727","key":"10.1016\/j.cdev.2023.203847_bb0010","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/s41586-018-0590-4","article-title":"Single-cell transcriptomics of 20 mouse organs creates a tabula muris","volume":"562","author":"Tabula Muris","year":"2018","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0015","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1038\/s41467-020-15647-5","article-title":"Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis","volume":"11","author":"Tsukui","year":"2020","journal-title":"Nat. Commun."},{"issue":"5","key":"10.1016\/j.cdev.2023.203847_bb0020","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1016\/j.cell.2018.02.001","article-title":"Mapping the mouse cell atlas by microwell-seq","volume":"172","author":"Han","year":"2018","journal-title":"Cell"},{"issue":"2","key":"10.1016\/j.cdev.2023.203847_bb0025","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.stem.2014.07.012","article-title":"Repair and regeneration of the respiratory system: complexity, plasticity, and mechanisms of lung stem cell function","volume":"15","author":"Hogan","year":"2014","journal-title":"Cell Stem Cell"},{"issue":"5","key":"10.1016\/j.cdev.2023.203847_bb0030","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.stem.2018.03.018","article-title":"Myoepithelial cells of submucosal glands can function as reserve stem cells to regenerate airways after injury","volume":"22","author":"Tata","year":"2018","journal-title":"Cell Stem Cell"},{"issue":"5","key":"10.1016\/j.cdev.2023.203847_bb0035","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1016\/j.stem.2018.03.017","article-title":"Submucosal gland myoepithelial cells are reserve stem cells that can regenerate mouse tracheal epithelium","volume":"22","author":"Lynch","year":"2018","journal-title":"Cell Stem Cell"},{"issue":"7718","key":"10.1016\/j.cdev.2023.203847_bb0040","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/s41586-018-0394-6","article-title":"A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte","volume":"560","author":"Plasschaert","year":"2018","journal-title":"Nature"},{"issue":"4","key":"10.1016\/j.cdev.2023.203847_bb0045","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/s41588-019-0346-6","article-title":"Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction","volume":"51","author":"Liu","year":"2019","journal-title":"Nat. Genet."},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0050","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1038\/s41467-020-17358-3","article-title":"Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis","volume":"11","author":"Strunz","year":"2020","journal-title":"Nat. Commun."},{"issue":"7718","key":"10.1016\/j.cdev.2023.203847_bb0055","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/s41586-018-0393-7","article-title":"A revised airway epithelial hierarchy includes CFTR-expressing ionocytes","volume":"560","author":"Montoro","year":"2018","journal-title":"Nature"},{"issue":"12","key":"10.1016\/j.cdev.2023.203847_bb0060","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"Gigascience"},{"issue":"13","key":"10.1016\/j.cdev.2023.203847_bb0065","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.cdev.2023.203847_bb0070","doi-asserted-by":"crossref","first-page":"979","DOI":"10.12688\/f1000research.73600.2","article-title":"Doublet identification in single-cell sequencing data using scDblFinder","volume":"10","author":"Germain","year":"2022","journal-title":"F1000Research"},{"issue":"12","key":"10.1016\/j.cdev.2023.203847_bb0075","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"issue":"11","key":"10.1016\/j.cdev.2023.203847_bb0080","doi-asserted-by":"crossref","first-page":"3447","DOI":"10.1093\/bioinformatics\/btaa092","article-title":"SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates","volume":"36","author":"Waas","year":"2020","journal-title":"Bioinformatics"},{"issue":"D1","key":"10.1016\/j.cdev.2023.203847_bb0085","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"UniProt","year":"2023","journal-title":"Nucleic Acids Res."},{"issue":"2","key":"10.1016\/j.cdev.2023.203847_bb0090","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/s41591-019-0750-6","article-title":"Regenerative lineages and immune-mediated pruning in lung cancer metastasis","volume":"26","author":"Laughney","year":"2020","journal-title":"Nat. Med."},{"issue":"7904","key":"10.1016\/j.cdev.2023.203847_bb0095","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/s41586-022-04541-3","article-title":"Human distal lung maps and lineage hierarchies reveal a bipotent progenitor","volume":"604","author":"Kadur Lakshminarasimha Murthy","year":"2022","journal-title":"Nature"},{"issue":"8","key":"10.1016\/j.cdev.2023.203847_bb0100","doi-asserted-by":"crossref","first-page":"2724","DOI":"10.1172\/JCI60519","article-title":"Building and maintaining the epithelium of the lung","volume":"122","author":"Rackley","year":"2012","journal-title":"J. Clin. Invest."},{"issue":"31","key":"10.1016\/j.cdev.2023.203847_bb0105","doi-asserted-by":"crossref","first-page":"12771","DOI":"10.1073\/pnas.0906850106","article-title":"Basal cells as stem cells of the mouse trachea and human airway epithelium","volume":"106","author":"Rock","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7536","key":"10.1016\/j.cdev.2023.203847_bb0110","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/nature13903","article-title":"p63(+)Krt5(+) distal airway stem cells are essential for lung regeneration","volume":"517","author":"Zuo","year":"2014","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0115","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.celrep.2015.06.011","article-title":"Clonal dynamics reveal two distinct populations of basal cells in slow-turnover airway epithelium","volume":"12","author":"Watson","year":"2015","journal-title":"Cell Rep."},{"issue":"9\u201310","key":"10.1016\/j.cdev.2023.203847_bb0120","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1242\/dmm.006031","article-title":"Airway basal stem cells: a perspective on their roles in epithelial homeostasis and remodeling","volume":"3","author":"Rock","year":"2010","journal-title":"Dis. Model. Mech."},{"issue":"7","key":"10.1016\/j.cdev.2023.203847_bb0125","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1634\/stemcells.2004-0197","article-title":"Aquaporin-3 expression in human fetal airway epithelial progenitor cells","volume":"23","author":"Avril-Delplanque","year":"2005","journal-title":"Stem Cells"},{"key":"10.1016\/j.cdev.2023.203847_bb0130","doi-asserted-by":"crossref","DOI":"10.3389\/falgy.2021.787128","article-title":"Airway basal cells, protectors of epithelial walls in health and respiratory diseases","volume":"2","author":"Ruysseveldt","year":"2021","journal-title":"Front Allergy"},{"issue":"6","key":"10.1016\/j.cdev.2023.203847_bb0135","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1016\/j.stem.2009.04.002","article-title":"The role of Scgb1a1+ Clara cells in the long-term maintenance and repair of lung airway, but not alveolar, epithelium","volume":"4","author":"Rawlins","year":"2009","journal-title":"Cell Stem Cell"},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0140","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.biocel.2009.09.002","article-title":"Clara cell: progenitor for the bronchiolar epithelium","volume":"42","author":"Reynolds","year":"2010","journal-title":"Int. J. Biochem. Cell Biol."},{"issue":"10","key":"10.1016\/j.cdev.2023.203847_bb0145","first-page":"2914","article-title":"SPDEF is required for mouse pulmonary goblet cell differentiation and regulates a network of genes associated with mucus production","volume":"119","author":"Chen","year":"2009","journal-title":"J. Clin. Invest."},{"issue":"7475","key":"10.1016\/j.cdev.2023.203847_bb0150","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/nature12777","article-title":"Dedifferentiation of committed epithelial cells into stem cells in vivo","volume":"503","author":"Tata","year":"2013","journal-title":"Nature"},{"issue":"10","key":"10.1016\/j.cdev.2023.203847_bb0155","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0048451","article-title":"Regeneration of alveolar type I and II cells from Scgb1a1-expressing cells following severe pulmonary damage induced by bleomycin and influenza","volume":"7","author":"Zheng","year":"2012","journal-title":"PLoS One"},{"issue":"31","key":"10.1016\/j.cdev.2023.203847_bb0160","doi-asserted-by":"crossref","first-page":"12592","DOI":"10.1073\/pnas.1204710109","article-title":"Neuroepithelial body microenvironment is a niche for a distinct subset of Clara-like precursors in the developing airways","volume":"109","author":"Guha","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"2","key":"10.1016\/j.cdev.2023.203847_bb0165","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.celrep.2017.03.051","article-title":"Uroplakin 3a(+) cells are a distinctive population of epithelial progenitors that contribute to airway maintenance and post-injury repair","volume":"19","author":"Guha","year":"2017","journal-title":"Cell Rep."},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0170","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.chest.2017.11.008","article-title":"Mucins, mucus, and goblet cells","volume":"154","author":"Ma","year":"2018","journal-title":"Chest"},{"issue":"3","key":"10.1016\/j.cdev.2023.203847_bb0175","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1165\/rcmb.2021-0548OC","article-title":"Secretory cells are the primary source of pIgR in small airways","volume":"67","author":"Blackburn","year":"2022","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"issue":"6","key":"10.1016\/j.cdev.2023.203847_bb0180","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/s41577-020-00477-9","article-title":"Regulation of immune responses by the airway epithelial cell landscape","volume":"21","author":"Hewitt","year":"2021","journal-title":"Nat. Rev. Immunol."},{"issue":"Suppl 3","key":"10.1016\/j.cdev.2023.203847_bb0185","doi-asserted-by":"crossref","first-page":"S143","DOI":"10.1513\/AnnalsATS.201802-128AW","article-title":"Airway epithelial differentiation and mucociliary clearance","volume":"15","author":"Whitsett","year":"2018","journal-title":"Ann. Am. Thorac. Soc."},{"issue":"9","key":"10.1016\/j.cdev.2023.203847_bb0190","doi-asserted-by":"crossref","first-page":"1948","DOI":"10.1002\/stem.1150","article-title":"Airway epithelial progenitors are region specific and show differential responses to bleomycin-induced lung injury","volume":"30","author":"Chen","year":"2012","journal-title":"Stem Cells"},{"issue":"6","key":"10.1016\/j.cdev.2023.203847_bb0195","doi-asserted-by":"crossref","first-page":"L1141","DOI":"10.1152\/ajplung.00032.2019","article-title":"Development of solitary chemosensory cells in the distal lung after severe influenza injury","volume":"316","author":"Rane","year":"2019","journal-title":"Am. J. Physiol. Lung Cell. Mol. Physiol."},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0200","doi-asserted-by":"crossref","first-page":"2485","DOI":"10.1038\/s41467-020-16239-z","article-title":"Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium","volume":"11","author":"Goldfarbmuren","year":"2020","journal-title":"Nat. Commun."},{"issue":"6274","key":"10.1016\/j.cdev.2023.203847_bb0205","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1126\/science.aad7969","article-title":"Pulmonary neuroendocrine cells function as airway sensors to control lung immune response","volume":"351","author":"Branchfield","year":"2016","journal-title":"Science"},{"issue":"2","key":"10.1016\/j.cdev.2023.203847_bb0210","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/j.cell.2019.09.010","article-title":"Rare pulmonary neuroendocrine cells are stem cells regulated by Rb, p53, and notch","volume":"179","author":"Ouadah","year":"2019","journal-title":"Cell"},{"issue":"7","key":"10.1016\/j.cdev.2023.203847_bb0215","doi-asserted-by":"crossref","first-page":"3025","DOI":"10.1172\/JCI68782","article-title":"Type 2 alveolar cells are stem cells in adult lung","volume":"123","author":"Barkauskas","year":"2013","journal-title":"J. Clin. Invest."},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0220","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/s12931-017-0635-5","article-title":"Fraction of MHCII and EpCAM expression characterizes distal lung epithelial cells for alveolar type 2 cell isolation","volume":"18","author":"Hasegawa","year":"2017","journal-title":"Respir. Res."},{"issue":"6","key":"10.1016\/j.cdev.2023.203847_bb0225","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2005.03.032","article-title":"Identification of bronchioalveolar stem cells in normal lung and lung cancer","volume":"121","author":"Kim","year":"2005","journal-title":"Cell"},{"issue":"1","key":"10.1016\/j.cdev.2023.203847_bb0230","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/S0002-9440(10)64169-7","article-title":"Terminal bronchioles harbor a unique airway stem cell population that localizes to the bronchoalveolar duct junction","volume":"161","author":"Giangreco","year":"2002","journal-title":"Am. J. Pathol."},{"issue":"12","key":"10.1016\/j.cdev.2023.203847_bb0235","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2019102099","article-title":"Bronchioalveolar stem cells are a main source for regeneration of distal lung epithelia in vivo","volume":"38","author":"Salwig","year":"2019","journal-title":"EMBO J."},{"key":"10.1016\/j.cdev.2023.203847_bb0240","doi-asserted-by":"crossref","first-page":"6727","DOI":"10.1038\/ncomms7727","article-title":"Plasticity of Hopx(+) type I alveolar cells to regenerate type II cells in the lung","volume":"6","author":"Jain","year":"2015","journal-title":"Nat. Commun."},{"issue":"11","key":"10.1016\/j.cdev.2023.203847_bb0245","doi-asserted-by":"crossref","DOI":"10.3390\/cells9112460","article-title":"Integrated single-cell RNA-sequencing analysis of aquaporin 5-expressing mouse lung epithelial cells identifies GPRC5A as a novel validated type I cell surface marker","volume":"9","author":"Horie","year":"2020","journal-title":"Cells"}],"updated-by":[{"DOI":"10.1016\/j.cdev.2023.203877","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T00:00:00Z","timestamp":1701388800000}}],"container-title":["Cells & Development"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667290123000232?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667290123000232?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,6,3]],"date-time":"2024-06-03T18:54:03Z","timestamp":1717440843000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667290123000232"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6]]},"references-count":49,"alternative-id":["S2667290123000232"],"URL":"https:\/\/doi.org\/10.1016\/j.cdev.2023.203847","relation":{"erratum":[{"id-type":"doi","id":"10.1016\/j.cdev.2023.203877","asserted-by":"object"}]},"ISSN":["2667-2901"],"issn-type":[{"value":"2667-2901","type":"print"}],"subject":[],"published":{"date-parts":[[2023,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Single-cell RNA sequencing of mouse lower respiratory tract epithelial cells: A meta-analysis","name":"articletitle","label":"Article Title"},{"value":"Cells & Development","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.cdev.2023.203847","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"203847"}}