{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T04:13:24Z","timestamp":1793938404149,"version":"4.8.0"},"reference-count":110,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T00:00:00Z","timestamp":1576108800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T00:00:00Z","timestamp":1576108800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Rev Nephrol"],"published-print":{"date-parts":[[2020,2]]},"DOI":"10.1038\/s41581-019-0227-3","type":"journal-article","created":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T15:10:09Z","timestamp":1576163409000},"page":"112-128","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":61,"title":["Using single-cell technologies to map the human immune system \u2014 implications for nephrology"],"prefix":"10.1038","volume":"16","author":[{"given":"Benjamin J.","family":"Stewart","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0936-0128","authenticated-orcid":false,"given":"John R.","family":"Ferdinand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3340-9828","authenticated-orcid":false,"given":"Menna R.","family":"Clatworthy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,12]]},"reference":[{"key":"227_CR1","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1126\/science.aan6828","volume":"358","author":"MJT Stubbington","year":"2017","unstructured":"Stubbington, M. J. T., Rozenblatt-Rosen, O., Regev, A. & Teichmann, S. A. Single-cell transcriptomics to explore the immune system in health and disease. Science 358, 58\u201363 (2017).","journal-title":"Science"},{"key":"227_CR2","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1038\/nri.2017.76","volume":"18","author":"E Papalexi","year":"2018","unstructured":"Papalexi, E. & Satija, R. Single-cell RNA sequencing to explore immune cell heterogeneity. Nat. Rev. Immunol. 18, 35\u201345 (2018).","journal-title":"Nat. Rev. Immunol."},{"key":"227_CR3","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1146\/annurev-immunol-042617-053214","volume":"37","author":"D Masopust","year":"2019","unstructured":"Masopust, D. & Soerens, A. G. Tissue-resident T cells and other resident leukocytes. Annu. Rev. Immunol. 37, 521\u2013546 (2019).","journal-title":"Annu. Rev. Immunol."},{"key":"227_CR4","doi-asserted-by":"publisher","first-page":"1387","DOI":"10.1681\/ASN.2014010117","volume":"25","author":"HJ Anders","year":"2014","unstructured":"Anders, H. J. & Schaefer, L. Beyond tissue injury-damage-associated molecular patterns, toll-like receptors, and inflammasomes also drive regeneration and fibrosis. J. Am. Soc. Nephrol. 25, 1387\u20131400 (2014).","journal-title":"J. Am. Soc. Nephrol."},{"key":"227_CR5","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1038\/s41581-019-0110-2","volume":"15","author":"PM Tang","year":"2019","unstructured":"Tang, P. M., Nikolic-Paterson, D. J. & Lan, H. Y. Macrophages: versatile players in renal inflammation and fibrosis. Nat. Rev. Nephrol. 15, 144\u2013158 (2019).","journal-title":"Nat. Rev. Nephrol."},{"key":"227_CR6","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1016\/S0092-8674(02)01201-1","volume":"111","author":"S Gordon","year":"2002","unstructured":"Gordon, S. Pattern recognition receptors: doubling up for the innate immune response. Cell 111, 927\u2013930 (2002).","journal-title":"Cell"},{"key":"227_CR7","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1038\/nrrheum.2009.136","volume":"5","author":"R Baccala","year":"2009","unstructured":"Baccala, R. et al. Sensors of the innate immune system: their mode of action. Nat. Rev. Rheumatol. 5, 448\u2013456 (2009).","journal-title":"Nat. Rev. Rheumatol."},{"key":"227_CR8","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1146\/annurev-immunol-032414-112043","volume":"33","author":"SR Woo","year":"2015","unstructured":"Woo, S. R., Corrales, L. & Gajewski, T. F. Innate immune recognition of cancer. Annu. Rev. Immunol. 33, 445\u2013474 (2015).","journal-title":"Annu. Rev. Immunol."},{"key":"227_CR9","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1136\/jclinpath-2017-204761","volume":"71","author":"E Mahe","year":"2018","unstructured":"Mahe, E., Pugh, T. & Kamel-Reid, S. T cell clonality assessment: past, present and future. J. Clin. Pathol. 71, 195\u2013200 (2018).","journal-title":"J. Clin. Pathol."},{"key":"227_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1146\/annurev.biochem.76.061705.090740","volume":"76","author":"JM Di Noia","year":"2007","unstructured":"Di Noia, J. M. & Neuberger, M. S. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 76, 1\u201322 (2007).","journal-title":"Annu. Rev. Biochem."},{"key":"227_CR11","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1146\/annurev-cellbio-100913-013254","volume":"30","author":"H Qi","year":"2014","unstructured":"Qi, H., Kastenmuller, W. & Germain, R. N. Spatiotemporal basis of innate and adaptive immunity in secondary lymphoid tissue. Annu. Rev. Cell. Dev. Biol. 30, 141\u2013167 (2014).","journal-title":"Annu. Rev. Cell. Dev. Biol."},{"key":"227_CR12","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-1-4939-6622-6_1","volume":"1525","author":"M Verma","year":"2017","unstructured":"Verma, M., Kulshrestha, S. & Puri, A. Genome sequencing. Methods Mol. Biol. 1525, 3\u201333 (2017).","journal-title":"Methods Mol. Biol."},{"key":"227_CR13","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0881-8","volume":"17","author":"A Conesa","year":"2016","unstructured":"Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 13 (2016).","journal-title":"Genome Biol."},{"key":"227_CR14","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1038\/nmeth.4380","volume":"14","author":"M Stoeckius","year":"2017","unstructured":"Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865\u2013868 (2017).","journal-title":"Nat. Methods"},{"key":"227_CR15","doi-asserted-by":"publisher","first-page":"519","DOI":"10.1038\/nmeth.3370","volume":"12","author":"IC Macaulay","year":"2015","unstructured":"Macaulay, I. C. et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat. Methods 12, 519\u2013522 (2015).","journal-title":"Nat. Methods"},{"key":"227_CR16","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/nbt.3129","volume":"33","author":"SS Dey","year":"2015","unstructured":"Dey, S. S., Kester, L., Spanjaard, B., Bienko, M. & van Oudenaarden, A. Integrated genome and transcriptome sequencing of the same cell. Nat. Biotechnol. 33, 285\u2013289 (2015).","journal-title":"Nat. Biotechnol."},{"key":"227_CR17","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1126\/science.aau0730","volume":"361","author":"J Cao","year":"2018","unstructured":"Cao, J. et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380\u20131385 (2018).","journal-title":"Science"},{"key":"227_CR18","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1126\/science.1247651","volume":"343","author":"DA Jaitin","year":"2014","unstructured":"Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776\u2013779 (2014).","journal-title":"Science"},{"key":"227_CR19","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1038\/nature13173","volume":"509","author":"B Treutlein","year":"2014","unstructured":"Treutlein, B. et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371\u2013375 (2014).","journal-title":"Nature"},{"key":"227_CR20","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","volume":"161","author":"EZ Macosko","year":"2015","unstructured":"Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202\u20131214 (2015).","journal-title":"Cell"},{"key":"227_CR21","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1016\/j.cell.2015.04.044","volume":"161","author":"AM Klein","year":"2015","unstructured":"Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187\u20131201 (2015).","journal-title":"Cell"},{"key":"227_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms14049","volume":"8","author":"GX Zheng","year":"2017","unstructured":"Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).","journal-title":"Nat. Commun."},{"key":"227_CR23","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1038\/nmeth.4407","volume":"14","author":"N Habib","year":"2017","unstructured":"Habib, N. et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat. Methods 14, 955\u2013958 (2017).","journal-title":"Nat. Methods"},{"key":"227_CR24","doi-asserted-by":"publisher","first-page":"871","DOI":"10.1016\/j.celrep.2018.09.006","volume":"25","author":"JB Cheng","year":"2018","unstructured":"Cheng, J. B. et al. Transcriptional programming of normal and inflamed human epidermis at single-cell resolution. Cell Rep. 25, 871\u2013883 (2018).","journal-title":"Cell Rep."},{"key":"227_CR25","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1126\/science.aam8999","volume":"360","author":"AB Rosenberg","year":"2018","unstructured":"Rosenberg, A. B. et al. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science 360, 176\u2013182 (2018).","journal-title":"Science"},{"key":"227_CR26","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1038\/s41581-018-0021-7","volume":"14","author":"SS Potter","year":"2018","unstructured":"Potter, S. S. Single-cell RNA sequencing for the study of development, physiology and disease. Nat. Rev. Nephrol. 14, 479\u2013492 (2018).","journal-title":"Nat. Rev. Nephrol."},{"key":"227_CR27","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1038\/nbt.3973","volume":"35","author":"VM Peterson","year":"2017","unstructured":"Peterson, V. M. et al. Multiplexed quantification of proteins and transcripts in single cells. Nat. Biotechnol. 35, 936\u2013939 (2017).","journal-title":"Nat. Biotechnol."},{"key":"227_CR28","doi-asserted-by":"publisher","first-page":"3625","DOI":"10.1242\/dev.151142","volume":"144","author":"M Adam","year":"2017","unstructured":"Adam, M., Potter, A. S. & Potter, S. S. Psychrophilic proteases dramatically reduce single-cell RNA-seq artifacts: a molecular atlas of kidney development. Development 144, 3625\u20133632 (2017).","journal-title":"Development"},{"key":"227_CR29","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1016\/j.cell.2017.07.022","volume":"170","author":"MR Berry","year":"2017","unstructured":"Berry, M. R. et al. Renal sodium gradient orchestrates a dynamic antibacterial defense zone. Cell 170, 860\u2013874.e19 (2017).","journal-title":"Cell"},{"key":"227_CR30","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1126\/science.aaf2403","volume":"353","author":"PL Stahl","year":"2016","unstructured":"Stahl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78\u201382 (2016).","journal-title":"Science"},{"key":"227_CR31","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1038\/s41592-018-0175-z","volume":"15","author":"S Codeluppi","year":"2018","unstructured":"Codeluppi, S. et al. Spatial organization of the somatosensory cortex revealed by osmFISH. Nat. Methods 15, 932\u2013935 (2018).","journal-title":"Nat. Methods"},{"key":"227_CR32","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1126\/science.1198704","volume":"332","author":"SC Bendall","year":"2011","unstructured":"Bendall, S. C. et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332, 687\u2013696 (2011).","journal-title":"Science"},{"key":"227_CR33","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1016\/j.cell.2015.05.047","volume":"162","author":"JH Levine","year":"2015","unstructured":"Levine, J. H. et al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 162, 184\u2013197 (2015).","journal-title":"Cell"},{"key":"227_CR34","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1038\/s41576-019-0093-7","volume":"20","author":"T Stuart","year":"2019","unstructured":"Stuart, T. & Satija, R. Integrative single-cell analysis. Nat. Rev. Genet. 20, 257\u2013272 (2019).","journal-title":"Nat. Rev. Genet."},{"key":"227_CR35","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/s41586-018-0698-6","volume":"563","author":"R Vento-Tormo","year":"2018","unstructured":"Vento-Tormo, R. et al. Single-cell reconstruction of the early maternal-fetal interface in humans. Nature 563, 347\u2013353 (2018).","journal-title":"Nature"},{"key":"227_CR36","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","volume":"36","author":"A Butler","year":"2018","unstructured":"Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411\u2013420 (2018).","journal-title":"Nat. Biotechnol."},{"key":"227_CR37","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1038\/nbt.4091","volume":"36","author":"L Haghverdi","year":"2018","unstructured":"Haghverdi, L., Lun, A. T. L., Morgan, M. D. & Marioni, J. C. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat. Biotechnol. 36, 421\u2013427 (2018).","journal-title":"Nat. Biotechnol."},{"key":"227_CR38","doi-asserted-by":"publisher","unstructured":"Polanski, K. et al. BBKNN: Fast batch alignment of single cell transcriptomes. Bioinformatics https:\/\/doi.org\/10.1093\/bioinformatics\/btz625 (2019).","DOI":"10.1093\/bioinformatics\/btz625"},{"key":"227_CR39","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"P Korsunsky","year":"2019","unstructured":"Korsunsky, P. et al. Fast, sensitive, and accurate integration of single cell data with Harmony. Nat.\u00a0Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"227_CR40","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/nmeth.3800","volume":"13","author":"MJ Stubbington","year":"2016","unstructured":"Stubbington, M. J. et al. T cell fate and clonality inference from single-cell transcriptomes. Nat. Methods 13, 329\u2013332 (2016).","journal-title":"Nat. Methods"},{"key":"227_CR41","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/s41586-018-0394-6","volume":"560","author":"LW Plasschaert","year":"2018","unstructured":"Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377\u2013381 (2018).","journal-title":"Nature"},{"key":"227_CR42","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-02926-5","volume":"9","author":"M Olah","year":"2018","unstructured":"Olah, M. et al. A transcriptomic atlas of aged human microglia. Nat. Commun. 9, 539 (2018).","journal-title":"Nat. Commun."},{"key":"227_CR43","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02659-x","volume":"9","author":"W Stephenson","year":"2018","unstructured":"Stephenson, W. et al. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Nat. Commun. 9, 791 (2018).","journal-title":"Nat. Commun."},{"key":"227_CR44","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.121718","volume":"3","author":"SF Farhadian","year":"2018","unstructured":"Farhadian, S. F. et al. Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV. JCI Insight 3, e121718 (2018).","journal-title":"JCI Insight"},{"key":"227_CR45","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/32588","volume":"392","author":"J Banchereau","year":"1998","unstructured":"Banchereau, J. & Steinman, R. M. Dendritic cells and the control of immunity. Nature 392, 245\u2013252 (1998).","journal-title":"Nature"},{"key":"227_CR46","doi-asserted-by":"publisher","DOI":"10.1126\/science.aah4573","volume":"356","author":"AC Villani","year":"2017","unstructured":"Villani, A. C. et al. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356, eaah4573 (2017).","journal-title":"Science"},{"key":"227_CR47","doi-asserted-by":"publisher","first-page":"2861","DOI":"10.1084\/jem.20161135","volume":"213","author":"G Breton","year":"2016","unstructured":"Breton, G. et al. Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs. J. Exp. Med. 213, 2861\u20132870 (2016).","journal-title":"J. Exp. Med."},{"key":"227_CR48","doi-asserted-by":"publisher","DOI":"10.1126\/science.aag3009","volume":"356","author":"P See","year":"2017","unstructured":"See, P. et al. Mapping the human DC lineage through the integration of high-dimensional techniques. Science 356, eaag3009 (2017).","journal-title":"Science"},{"key":"227_CR49","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-05784-3","volume":"9","author":"F Wimmers","year":"2018","unstructured":"Wimmers, F. et al. Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells. Nat. Commun. 9, 3317 (2018).","journal-title":"Nat. Commun."},{"key":"227_CR50","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1084\/jem.20021553","volume":"197","author":"L Bennett","year":"2003","unstructured":"Bennett, L. et al. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J. Exp. Med. 197, 711\u2013723 (2003).","journal-title":"J. Exp. Med."},{"key":"227_CR51","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1038\/nature14468","volume":"523","author":"EF McKinney","year":"2015","unstructured":"McKinney, E. F., Lee, J. C., Jayne, D. R., Lyons, P. A. & Smith, K. G. T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection. Nature 523, 612\u2013616 (2015).","journal-title":"Nature"},{"key":"227_CR52","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/s41592-018-0082-3","volume":"15","author":"I Lindeman","year":"2018","unstructured":"Lindeman, I. et al. BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq. Nat. Methods 15, 563\u2013565 (2018).","journal-title":"Nat. Methods"},{"key":"227_CR53","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1093\/bioinformatics\/btw631","volume":"33","author":"S Canzar","year":"2017","unstructured":"Canzar, S., Neu, K. E., Tang, Q., Wilson, P. C. & Khan, A. A. BASIC: BCR assembly from single cells. Bioinformatics 33, 425\u2013427 (2017).","journal-title":"Bioinformatics"},{"key":"227_CR54","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aal2192","volume":"2","author":"T Lonnberg","year":"2017","unstructured":"Lonnberg, T. et al. Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1\/Tfh fate bifurcation in malaria. Sci. Immunol. 2, eaal2192 (2017).","journal-title":"Sci. Immunol."},{"key":"227_CR55","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/s41590-018-0294-9","volume":"20","author":"N Li","year":"2019","unstructured":"Li, N. et al. Memory CD4(+) T cells are generated in the human fetal intestine. Nat. Immunol. 20, 301\u2013312 (2019).","journal-title":"Nat. Immunol."},{"key":"227_CR56","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/ni.3368","volume":"17","author":"AK Bjorklund","year":"2016","unstructured":"Bjorklund, A. K. et al. The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Nat. Immunol. 17, 451\u2013460 (2016).","journal-title":"Nat. Immunol."},{"key":"227_CR57","doi-asserted-by":"publisher","first-page":"971","DOI":"10.1016\/j.immuni.2018.09.009","volume":"49","author":"A Crinier","year":"2018","unstructured":"Crinier, A. et al. High-dimensional single-cell analysis identifies organ-specific signatures and conserved NK cell subsets in humans and mice. Immunity 49, 971\u2013986.e5 (2018).","journal-title":"Immunity"},{"key":"227_CR58","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1016\/j.immuni.2006.10.011","volume":"25","author":"M Bajenoff","year":"2006","unstructured":"Bajenoff, M. et al. Stromal cell networks regulate lymphocyte entry, migration, and territoriality in lymph nodes. Immunity 25, 989\u20131001 (2006).","journal-title":"Immunity"},{"key":"227_CR59","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1034\/j.1600-065X.2000.00618.x","volume":"176","author":"JG Cyster","year":"2000","unstructured":"Cyster, J. G. et al. Follicular stromal cells and lymphocyte homing to follicles. Immunol. Rev. 176, 181\u2013193 (2000).","journal-title":"Immunol. Rev."},{"key":"227_CR60","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/nri2588","volume":"9","author":"SN Mueller","year":"2009","unstructured":"Mueller, S. N. & Germain, R. N. Stromal cell contributions to the homeostasis and functionality of the immune system. Nat. Rev. Immunol. 9, 618\u2013629 (2009).","journal-title":"Nat. Rev. Immunol."},{"key":"227_CR61","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1016\/j.immuni.2018.04.006","volume":"48","author":"LB Rodda","year":"2018","unstructured":"Rodda, L. B. et al. Single-cell RNA sequencing of lymph node stromal cells reveals niche-associated heterogeneity. Immunity 48, 1014\u20131028.e6 (2018).","journal-title":"Immunity"},{"key":"227_CR62","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1038\/nrneph.2014.170","volume":"10","author":"NM Rogers","year":"2014","unstructured":"Rogers, N. M., Ferenbach, D. A., Isenberg, J. S., Thomson, A. W. & Hughes, J. Dendritic cells and macrophages in the kidney: a spectrum of good and evil. Nat. Rev. Nephrol. 10, 625\u2013643 (2014).","journal-title":"Nat. Rev. Nephrol."},{"key":"227_CR63","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/nature13150","volume":"509","author":"T Olszak","year":"2014","unstructured":"Olszak, T. et al. Protective mucosal immunity mediated by epithelial CD1d and IL-10. Nature 509, 497\u2013502 (2014).","journal-title":"Nature"},{"key":"227_CR64","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/j.cell.2015.08.061","volume":"163","author":"T Sano","year":"2015","unstructured":"Sano, T. et al. An IL-23R\/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses. Cell 163, 381\u2013393 (2015).","journal-title":"Cell"},{"key":"227_CR65","doi-asserted-by":"publisher","first-page":"1153","DOI":"10.1038\/s41591-019-0468-5","volume":"25","author":"FA Vieira Braga","year":"2019","unstructured":"Vieira Braga, F. A. et al. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153\u20131163 (2019).","journal-title":"Nat. Med."},{"key":"227_CR66","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/s41586-018-0393-7","volume":"560","author":"DT Montoro","year":"2018","unstructured":"Montoro, D. T. et al. A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature 560, 319\u2013324 (2018).","journal-title":"Nature"},{"key":"227_CR67","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06318-7","volume":"9","author":"SA MacParland","year":"2018","unstructured":"MacParland, S. A. et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat. Commun. 9, 4383 (2018).","journal-title":"Nat. Commun."},{"key":"227_CR68","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1126\/science.1194637","volume":"330","author":"F Ginhoux","year":"2010","unstructured":"Ginhoux, F. et al. Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science 330, 841\u2013845 (2010).","journal-title":"Science"},{"key":"227_CR69","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1126\/science.1219179","volume":"336","author":"C Schulz","year":"2012","unstructured":"Schulz, C. et al. A lineage of myeloid cells independent of Myb and hematopoietic stem cells. Science 336, 86\u201390 (2012).","journal-title":"Science"},{"key":"227_CR70","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1084\/jem.20161375","volume":"214","author":"JA Noelia A-Gonzalez","year":"2017","unstructured":"Noelia A-Gonzalez, J. A. et al. Phagocytosis imprints heterogeneity in tissue-resident macrophages. J. Exp. Med. 214, 1281\u20131296 (2017).","journal-title":"J. Exp. Med."},{"key":"227_CR71","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1126\/science.1262110","volume":"348","author":"GTEx Consortium Human genomics","year":"2015","unstructured":"GTEx Consortium Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648\u2013660 (2015).","journal-title":"Science"},{"key":"227_CR72","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1016\/j.cell.2017.03.050","volume":"169","author":"M Hulsmans","year":"2017","unstructured":"Hulsmans, M. et al. Macrophages facilitate electrical conduction in the heart. Cell 169, 510\u2013522.e20 (2017).","journal-title":"Cell"},{"key":"227_CR73","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1016\/j.cell.2014.04.050","volume":"158","author":"PA Muller","year":"2014","unstructured":"Muller, P. A. et al. Crosstalk between muscularis macrophages and enteric neurons regulates gastrointestinal motility. Cell 158, 300\u2013313 (2014).","journal-title":"Cell"},{"key":"227_CR74","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1016\/j.cell.2018.07.048","volume":"175","author":"S De Schepper","year":"2018","unstructured":"De Schepper, S. et al. Self-maintaining gut macrophages are essential for intestinal homeostasis. Cell 175, 400\u2013415.e13 (2018).","journal-title":"Cell"},{"key":"227_CR75","doi-asserted-by":"publisher","first-page":"1031","DOI":"10.1016\/j.cell.2018.09.009","volume":"175","author":"M Cohen","year":"2018","unstructured":"Cohen, M. et al. Lung single-cell signaling interaction map reveals basophil role in macrophage imprinting. Cell 175, 1031\u20131044.e18 (2018).","journal-title":"Cell"},{"key":"227_CR76","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/nature24489","volume":"551","author":"AL Haber","year":"2017","unstructured":"Haber, A. L. et al. A single-cell survey of the small intestinal epithelium. Nature 551, 333\u2013339 (2017).","journal-title":"Nature"},{"key":"227_CR77","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/nature14052","volume":"520","author":"S Naik","year":"2015","unstructured":"Naik, S. et al. Commensal-dendritic-cell interaction specifies a unique protective skin immune signature. Nature 520, 104\u2013108 (2015).","journal-title":"Nature"},{"key":"227_CR78","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1016\/j.cell.2019.08.008","volume":"178","author":"JC Martin","year":"2019","unstructured":"Martin, J. C. et al. Single-cell analysis of Crohn\u2019s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy. Cell 178, 1493\u20131508.e20 (2019).","journal-title":"Cell"},{"key":"227_CR79","doi-asserted-by":"publisher","first-page":"7285","DOI":"10.1073\/pnas.1507125112","volume":"112","author":"S Darmanis","year":"2015","unstructured":"Darmanis, S. et al. A survey of human brain transcriptome diversity at the single cell level. Proc. Natl Acad. Sci. USA 112, 7285\u20137290 (2015).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"227_CR80","doi-asserted-by":"publisher","first-page":"1138","DOI":"10.1126\/science.aaa1934","volume":"347","author":"A Zeisel","year":"2015","unstructured":"Zeisel, A. et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347, 1138\u20131142 (2015).","journal-title":"Science"},{"key":"227_CR81","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1016\/j.cell.2017.05.018","volume":"169","author":"H Keren-Shaul","year":"2017","unstructured":"Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer\u2019s disease. Cell 169, 1276\u20131290.e17 (2017).","journal-title":"Cell"},{"key":"227_CR82","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1038\/s41586-019-0924-x","volume":"566","author":"T Masuda","year":"2019","unstructured":"Masuda, T. et al. Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution. Nature 566, 388\u2013392 (2019).","journal-title":"Nature"},{"key":"227_CR83","doi-asserted-by":"publisher","first-page":"1544","DOI":"10.1016\/j.jalz.2018.07.078","volume":"14","author":"M Olah","year":"2018","unstructured":"Olah, M. et al. A single cell-based atlas of human microglial states reveals associations with neurological disorders and histopathological features of the aging brain. Alzheimers Dement. 14, 1544\u20131545 (2018).","journal-title":"Alzheimers Dement."},{"key":"227_CR84","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1016\/j.cell.2017.05.035","volume":"169","author":"C Zheng","year":"2017","unstructured":"Zheng, C. et al. Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell 169, 1342\u20131356.e16 (2017).","journal-title":"Cell"},{"key":"227_CR85","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/s41591-018-0266-5","volume":"25","author":"W Scheper","year":"2019","unstructured":"Scheper, W. et al. Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers. Nat. Med. 25, 89\u201394 (2019).","journal-title":"Nat. Med."},{"key":"227_CR86","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1016\/j.cell.2018.11.043","volume":"176","author":"H Li","year":"2019","unstructured":"Li, H. et al. Dysfunctional CD8 T cells form a proliferative, dynamically regulated compartment within human melanoma. Cell 176, 775\u2013789.e18 (2019).","journal-title":"Cell"},{"key":"227_CR87","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/BF00586235","volume":"350","author":"H Koepsell","year":"1974","unstructured":"Koepsell, H., Nicholson, W. A., Kriz, W. & Hohling, H. J. Measurements of exponential gradients of sodium and chlorine in the rat kidney medulla using the electron microprobe. Pflugers Arch. 350, 167\u2013184 (1974).","journal-title":"Pflugers Arch."},{"key":"227_CR88","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1056\/NEJMc1505505","volume":"373","author":"MA Knepper","year":"2015","unstructured":"Knepper, M. A., Kwon, T. H. & Nielsen, S. Molecular physiology of water balance. N. Engl. J. Med. 373, 196 (2015).","journal-title":"N. Engl. J. Med."},{"key":"227_CR89","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1172\/JCI104567","volume":"41","author":"H Levitin","year":"1962","unstructured":"Levitin, H., Goodman, A., Pigeon, G. & Epstein, F. H. Composition of the renal medulla during water diuresis. J. Clin. Invest. 41, 1145\u20131151 (1962).","journal-title":"J. Clin. Invest."},{"key":"227_CR90","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1126\/science.aar2131","volume":"360","author":"J Park","year":"2018","unstructured":"Park, J. et al. Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. Science 360, 758\u2013763 (2018).","journal-title":"Science"},{"key":"227_CR91","doi-asserted-by":"publisher","first-page":"E9989","DOI":"10.1073\/pnas.1710964114","volume":"114","author":"L Chen","year":"2017","unstructured":"Chen, L. et al. Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. Proc. Natl Acad. Sci. USA 114, E9989\u2013E9998 (2017).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"227_CR92","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1016\/j.cell.2018.06.052","volume":"174","author":"DA Cusanovich","year":"2018","unstructured":"Cusanovich, D. A. et al. A single-cell atlas of in vivo mammalian chromatin accessibility. Cell 174, 1309\u20131324.e18 (2018).","journal-title":"Cell"},{"key":"227_CR93","doi-asserted-by":"publisher","unstructured":"Sivakamasundari, V. et al. Comprehensive cell type specific transcriptomics of the human kidney. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/238063 (2017)","DOI":"10.1101\/238063"},{"key":"227_CR94","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":"227_CR95","doi-asserted-by":"publisher","first-page":"736","DOI":"10.1016\/j.cell.2017.04.016","volume":"169","author":"S Chevrier","year":"2017","unstructured":"Chevrier, S. et al. An immune atlas of clear cell renal cell carcinoma. Cell 169, 736\u2013749.e18 (2017).","journal-title":"Cell"},{"key":"227_CR96","doi-asserted-by":"publisher","first-page":"dev164038","DOI":"10.1242\/dev.164038","volume":"145","author":"R Menon","year":"2018","unstructured":"Menon, R. et al. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development 145, dev164038 (2018).","journal-title":"Development"},{"key":"227_CR97","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1681\/ASN.2017080887","volume":"29","author":"NO Lindstrom","year":"2018","unstructured":"Lindstrom, N. O. et al. Conserved and divergent features of human and mouse kidney organogenesis. J. Am. Soc. Nephrol. 29, 785\u2013805 (2018).","journal-title":"J. Am. Soc. Nephrol."},{"key":"227_CR98","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0615-0","volume":"11","author":"AN Combes","year":"2019","unstructured":"Combes, A. N., Zappia, L., Er, P. X., Oshlack, A. & Little, M. H. Single-cell analysis reveals congruence between kidney organoids and human fetal kidney. Genome Med 11, 3 (2019).","journal-title":"Genome Med"},{"key":"227_CR99","doi-asserted-by":"publisher","first-page":"aaf4238","DOI":"10.1126\/science.aaf4238","volume":"353","author":"E Mass","year":"2016","unstructured":"Mass, E. et al. Specification of tissue-resident macrophages during organogenesis. Science 353, aaf4238 (2016).","journal-title":"Science"},{"key":"227_CR100","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1136\/jcp.2010.082024","volume":"64","author":"C Bellan","year":"2011","unstructured":"Bellan, C. et al. Analysis of the IgVH genes in T cell-mediated and antibody-mediated rejection of the kidney graft. J. Clin. Pathol. 64, 47\u201353 (2011).","journal-title":"J. Clin. Pathol."},{"key":"227_CR101","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.semnephrol.2017.09.005","volume":"38","author":"AF Malone","year":"2018","unstructured":"Malone, A. F., Wu, H. & Humphreys, B. D. Bringing renal biopsy interpretation into the molecular age with single-cell RNA sequencing. Semin. Nephrol. 38, 31\u201339 (2018).","journal-title":"Semin. Nephrol."},{"key":"227_CR102","doi-asserted-by":"publisher","first-page":"93009","DOI":"10.1172\/jci.insight.93009","volume":"2,","author":"E Der","year":"2017","unstructured":"Der, E. et al. Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis. JCI Insight 2, 93009 (2017).","journal-title":"JCI Insight"},{"key":"227_CR103","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1038\/s41590-019-0398-x","volume":"20","author":"A Arazi","year":"2019","unstructured":"Arazi, A. et al. The immune cell landscape in kidneys of patients with lupus nephritis. Nat. Immunol. 20, 902\u2013914 (2019).","journal-title":"Nat. Immunol."},{"key":"227_CR104","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1038\/s41590-019-0386-1","volume":"20","author":"E Der","year":"2019","unstructured":"Der, E. et al. Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. Nat. Immunol. 20, 915\u2013927 (2019).","journal-title":"Nat. Immunol."},{"key":"227_CR105","doi-asserted-by":"publisher","first-page":"2069","DOI":"10.1681\/ASN.2018020125","volume":"29","author":"H Wu","year":"2018","unstructured":"Wu, H. et al. Single-cell transcriptomics of a human kidney allograft biopsy specimen defines a diverse inflammatory response. J. Am. Soc. Nephrol. 29, 2069\u20132080 (2018).","journal-title":"J. Am. Soc. Nephrol."},{"key":"227_CR106","doi-asserted-by":"publisher","first-page":"717","DOI":"10.4049\/jimmunol.0903589","volume":"185","author":"O Thaunat","year":"2010","unstructured":"Thaunat, O. et al. Chronic rejection triggers the development of an aggressive intragraft immune response through recapitulation of lymphoid organogenesis. J. Immunol. 185, 717\u2013728 (2010).","journal-title":"J. Immunol."},{"key":"227_CR107","doi-asserted-by":"publisher","first-page":"1648","DOI":"10.1097\/TP.0b013e3181735723","volume":"85","author":"O Thaunat","year":"2008","unstructured":"Thaunat, O. et al. B cell survival in intragraft tertiary lymphoid organs after rituximab therapy. Transplantation 85, 1648\u20131653 (2008).","journal-title":"Transplantation"},{"key":"227_CR108","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1002\/cncr.21951","volume":"107","author":"WS Webster","year":"2006","unstructured":"Webster, W. S. et al. Mononuclear cell infiltration in clear-cell renal cell carcinoma independently predicts patient survival. Cancer 107, 46\u201353 (2006).","journal-title":"Cancer"},{"key":"227_CR109","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1126\/science.aat1699","volume":"361","author":"MD Young","year":"2018","unstructured":"Young, M. D. et al. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 361, 594\u2013599 (2018).","journal-title":"Science"},{"key":"227_CR110","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.27041","volume":"6","author":"A Regev","year":"2017","unstructured":"Regev, A. et al. The Human Cell Atlas. eLife 6, e27041 (2017).","journal-title":"eLife"}],"container-title":["Nature Reviews Nephrology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/s41581-019-0227-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41581-019-0227-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/s41581-019-0227-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,23]],"date-time":"2023-09-23T22:47:22Z","timestamp":1695509242000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41581-019-0227-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12,12]]},"references-count":110,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,2]]}},"alternative-id":["227"],"URL":"https:\/\/doi.org\/10.1038\/s41581-019-0227-3","relation":{},"ISSN":["1759-5061","1759-507X"],"issn-type":[{"value":"1759-5061","type":"print"},{"value":"1759-507X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12,12]]},"assertion":[{"value":"28 October 2019","order":1,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 December 2019","order":2,"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"}}]}}