{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T05:13:24Z","timestamp":1792214004590,"version":"4.4.0"},"reference-count":200,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2024,4,11]],"date-time":"2024-04-11T00:00:00Z","timestamp":1712793600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biosensors"],"abstract":"<jats:p>Single-cell RNA sequencing is a high-throughput novel method that provides transcriptional profiling of individual cells within biological samples. This method typically uses microfluidics systems to uncover the complex intercellular communication networks and biological pathways buried within highly heterogeneous cell populations in tissues. One important application of this technology sits in the fields of organ and stem cell transplantation, where complications such as graft rejection and other post-transplantation life-threatening issues may occur. In this review, we first focus on research in which single-cell RNA sequencing is used to study the transcriptional profile of transplanted tissues. This technology enables the analysis of the donor and recipient cells and identifies cell types and states associated with transplant complications and pathologies. We also review the use of single-cell RNA sequencing in stem cell implantation. This method enables studying the heterogeneity of normal and pathological stem cells and the heterogeneity in cell populations. With their remarkably rapid pace, the single-cell RNA sequencing methodologies will potentially result in breakthroughs in clinical transplantation in the coming years.<\/jats:p>","DOI":"10.3390\/bios14040189","type":"journal-article","created":{"date-parts":[[2024,4,11]],"date-time":"2024-04-11T03:29:04Z","timestamp":1712806144000},"page":"189","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Single-Cell RNA Sequencing in Organ and Cell Transplantation"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0729-7770","authenticated-orcid":false,"given":"Roozbeh","family":"Abedini-Nassab","sequence":"first","affiliation":[{"name":"Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatemeh","family":"Taheri","sequence":"additional","affiliation":[{"name":"Biomedical Engineering Department, University of Neyshabur, Neyshabur P.O. Box 9319774446, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6941-9797","authenticated-orcid":false,"given":"Ali","family":"Emamgholizadeh","sequence":"additional","affiliation":[{"name":"Faculty of Mechanical Engineering, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4227-171X","authenticated-orcid":false,"given":"Hossein","family":"Naderi-Manesh","sequence":"additional","affiliation":[{"name":"Department of Nanobiotechnology, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran"},{"name":"Department of Biophysics, Faculty of Bioscience, Tarbiat Modares University, Tehran P.O. Box 1411944961, Iran"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,4,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/s41392-022-00990-4","article-title":"High-throughput single-cell sequencing in cancer research","volume":"7","author":"Jia","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Eum, H.H., Jeong, D., Kim, N., Jo, A., Na, M., Kang, H., Hong, Y., Kong, J.S., Jeong, G.H., and Yoo, S.A. (2024). Single-cell RNA sequencing reveals myeloid and T cell co-stimulation mediated by IL-7 anti-cancer immunotherapy. Br. J. Cancer.","DOI":"10.1038\/s41416-024-02617-7"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1038\/s41593-020-00794-1","article-title":"Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia","volume":"24","author":"Eze","year":"2021","journal-title":"Nat. Neurosci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/s41593-023-01549-4","article-title":"Single-cell transcriptomics reveals that glial cells integrate homeostatic and circadian processes to drive sleep\u2013wake cycles","volume":"27","author":"Dopp","year":"2024","journal-title":"Nat. Neurosci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1681\/ASN.2018020125","article-title":"Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response","volume":"29","author":"Wu","year":"2018","journal-title":"J. Am. Soc. Nephrol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nri.2017.76","article-title":"Single-cell RNA sequencing to explore immune cell heterogeneity","volume":"18","author":"Papalexi","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"832573","DOI":"10.3389\/fimmu.2022.832573","article-title":"Single-Cell RNA Sequencing Identifies Intra-Graft Population Heterogeneity in Acute Heart Allograft Rejection in Mouse","volume":"13","author":"Tang","year":"2022","journal-title":"Front. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1097\/TP.0000000000004763","article-title":"Partners in Crime: Inferring Cell-to-cell Interactions in Kidney Allograft Rejection from Single-cell RNA Sequencing","volume":"108","author":"Thareja","year":"2024","journal-title":"Transplantation"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.devcel.2020.11.010","article-title":"Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn\u2019s Disease","volume":"55","author":"Elmentaite","year":"2020","journal-title":"Dev. Cell"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.stemcr.2019.10.001","article-title":"Transcriptional Profiling of Xenogeneic Transplants: Examining Human Pluripotent Stem Cell-Derived Grafts in the Rodent Brain","volume":"13","author":"Bye","year":"2019","journal-title":"Stem Cell Rep."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Abedini-Nassab, R., Pouryosef Miandoab, M., and Sasmaz, M. (2021). Microfluidic Synthesis, Control, and Sensing of Magnetic Nanoparticles: A Review. Micromachines, 12.","DOI":"10.3390\/mi12070768"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1038\/s41467-021-21892-z","article-title":"Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis","volume":"12","author":"Mantri","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1111\/aor.14151","article-title":"Designer organs: The future of personalized transplantation","volume":"46","author":"Buchwald","year":"2022","journal-title":"Artif. Organs"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"750754","DOI":"10.3389\/fimmu.2021.750754","article-title":"Advanced Genomics-Based Approaches for Defining Allograft Rejection with Single Cell Resolution","volume":"12","author":"Shi","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13287-018-1005-z","article-title":"Mechanisms underlying dental-derived stem cell-mediated neurorestoration in neurodegenerative disorders","volume":"9","author":"Raza","year":"2018","journal-title":"Stem Cell Res. Ther."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/978-1-62703-508-8_20","article-title":"Serial orthotopic transplantation of epithelial tumors in single-cell suspension","volume":"1035","author":"McCauley","year":"2013","journal-title":"Methods Mol. Biol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Kim, H.K., Ha, T.W., and Lee, M.R. (2021). Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22115988"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1093\/clinchem\/48.10.1819","article-title":"The history and future of the fluorescence activated cell sorter and flow cytometry: A view from Stanford","volume":"48","author":"Herzenberg","year":"2002","journal-title":"Clin. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1063\/1.1685647","article-title":"Fluorescence activated cell sorting","volume":"43","author":"Bonner","year":"1972","journal-title":"Rev. Sci. Instrum."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5.1.1","DOI":"10.1002\/cpim.40","article-title":"Flow Cytometry: An Overview","volume":"120","author":"McKinnon","year":"2018","journal-title":"Curr. Protoc. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s40648-022-00220-0","article-title":"Real-time irradiation system using patterned light to actuate light-driven on-chip gel actuators","volume":"9","author":"Koike","year":"2022","journal-title":"Robomech J."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Adam, G., Chidambaram, S., Reddy, S.S., Ramani, K., and Cappelleri, D.J. (2021). Towards a Comprehensive and Robust Micromanipulation System with Force-Sensing and VR Capabilities. Micromachines, 12.","DOI":"10.3390\/mi12070784"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.reth.2019.03.004","article-title":"Effect of liquid flow by pipetting during medium change on deformation of hiPSC aggregates","volume":"12","author":"Kato","year":"2019","journal-title":"Regen. Ther."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1039\/b605937f","article-title":"Dynamic single cell culture array","volume":"6","author":"Wu","year":"2006","journal-title":"Lab. Chip"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3751","DOI":"10.1039\/C7AY00656J","article-title":"Microfluidic hydrodynamic trapping for single cell analysis: Mechanisms, methods and applications","volume":"9","author":"Narayanamurthy","year":"2017","journal-title":"Anal. Methods"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Luan, Q., Macaraniag, C., Zhou, J., and Papautsky, I. (2020). Microfluidic systems for hydrodynamic trapping of cells and clusters. Biomicrofluidics, 14.","DOI":"10.1063\/5.0002866"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Abedini-Nassab, R. (2020). Magnetophoretic Circuit Biocompatibility. J. Mech. Med. Biol., 20.","DOI":"10.1142\/S0219519420500505"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Ahmadi, F., Tran, H., Letourneau, N., Little, S.R., Fortin, A., Moraitis, A.N., and Shih, S.C.C. (2024). An Automated Single-Cell Droplet-Digital Microfluidic Platform for Monoclonal Antibody Discovery. Small.","DOI":"10.1002\/smll.202308950"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"9668","DOI":"10.1109\/JSEN.2020.2992551","article-title":"A Microfluidic Platform Equipped with Magnetic Nano Films for Organizing Bio-Particle Arrays and Long-Term Studies","volume":"20","author":"Mahdaviyan","year":"2020","journal-title":"IEEE Sens. J."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"6380","DOI":"10.1038\/s41598-022-10122-1","article-title":"High-throughput precise particle transport at single-particle resolution in a three-dimensional magnetic field for highly sensitive bio-detection","volume":"12","author":"Shourabi","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Zhou, A., Chen, S., Lum, G.Z., and Zhang, X. (2022). A perspective on magnetic microfluidics: Towards an intelligent future. Biomicrofluidics, 16.","DOI":"10.1063\/5.0079464"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"13451","DOI":"10.1021\/acs.analchem.8b03272","article-title":"Magnetic-Based Microfluidic Device for On-Chip Isolation and Detection of Tumor-Derived Exosomes","volume":"90","author":"Xu","year":"2018","journal-title":"Anal. Chem."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1039\/D1LC01104A","article-title":"A novel magnetophoretic-based device for magnetometry and separation of single magnetic particles and magnetized cells","volume":"22","author":"Ding","year":"2022","journal-title":"Lab. Chip"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1007\/s10404-023-02702-y","article-title":"Unidirectional particle transport in microfluidic chips operating in a tri-axial magnetic field for particle concentration and bio-analyte detection","volume":"28","author":"Sadeghidelouei","year":"2023","journal-title":"Microfluid. Nanofluidics"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2804","DOI":"10.1038\/s41467-020-16630-w","article-title":"Precise capture and dynamic relocation of nanoparticulate biomolecules through dielectrophoretic enhancement by vertical nanogap architectures","volume":"11","author":"Yu","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"11988","DOI":"10.1038\/s41598-019-48198-x","article-title":"A flow through device for simultaneous dielectrophoretic cell trapping and AC electroporation","volume":"9","author":"Punjiya","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"R705","DOI":"10.1088\/0953-8984\/17\/28\/R01","article-title":"Electrowetting: From basics to applications","volume":"17","author":"Mugele","year":"2005","journal-title":"J. Physics Condens. Matter"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1007\/s10404-022-02544-0","article-title":"Quantifying the dielectrophoretic force on colloidal particles in microfluidic devices","volume":"26","author":"Wirfel","year":"2022","journal-title":"Microfluid. Nanofluidics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2441","DOI":"10.1038\/s41596-023-00844-5","article-title":"Acoustic tweezers for high-throughput single-cell analysis","volume":"18","author":"Yang","year":"2023","journal-title":"Nat. Protoc."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"198","DOI":"10.2174\/1872210515666210428134424","article-title":"Nanotechnology and Acoustics in Medicine and Biology","volume":"16","author":"Emami","year":"2022","journal-title":"Recent Pat. Nanotechnol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/s43586-022-00109-7","article-title":"Acoustofluidics for biomedical applications","volume":"2","author":"Rufo","year":"2022","journal-title":"Nat. Rev. Methods Primers"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"105603","DOI":"10.1016\/j.ultsonch.2021.105603","article-title":"Particle separation in microfluidics using different modal ultrasonic standing waves","volume":"75","author":"Zhang","year":"2021","journal-title":"Ultrason. Sonochem."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1039\/C8LC00196K","article-title":"An acoustofluidic trap and transfer approach for organizing a high density single cell array","volume":"18","author":"Ohiri","year":"2018","journal-title":"Lab. Chip"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"022501","DOI":"10.1088\/2515-7647\/acb57b","article-title":"Roadmap for optical tweezers","volume":"5","author":"Volpe","year":"2023","journal-title":"J. Phys. Photonics"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nbt1050","article-title":"Microfluidic sorting of mammalian cells by optical force switching","volume":"23","author":"Wang","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"22630","DOI":"10.1038\/srep22630","article-title":"Self-Locking Optoelectronic Tweezers for Single-Cell and Microparticle Manipulation across a Large Area in High Conductivity Media","volume":"6","author":"Yang","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1126\/science.abj3013","article-title":"High-speed fluorescence image-enabled cell sorting","volume":"375","author":"Schraivogel","year":"2022","journal-title":"Science"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1111\/1556-4029.15379","article-title":"Droplet-based optical trapping for cell separation in mock forensic samples","volume":"69","author":"Valle","year":"2024","journal-title":"J. Forensic Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1117\/1.429966","article-title":"Cell viability in optical tweezers: High power red laser diode versus Nd:YAG laser","volume":"5","author":"Schneckenburger","year":"2000","journal-title":"J. Biomed. Opt."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"12355","DOI":"10.1038\/s41598-021-91219-x","article-title":"Selective control of the contact and transport between droplet pairs by electrowetting-on-dielectric for droplet-array sandwiching technology","volume":"11","author":"Konishi","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"2465","DOI":"10.1016\/0032-3861(96)85360-2","article-title":"Electrowetting of water and aqueous solutions on poly(ethylene terephthalate) insulating films","volume":"37","author":"Vallet","year":"1996","journal-title":"Polymer"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"341425","DOI":"10.1016\/j.aca.2023.341425","article-title":"Magnetophoretic circuits: A review of device designs and implementation for precise single-cell manipulation","volume":"1272","author":"Sadeghidelouei","year":"2023","journal-title":"Anal. Chim. Acta"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Abedini-Nassab, R. (2023). Magnetomicrofluidic Circuits for Single-Bioparticle Transport, Springer Nature.","DOI":"10.1007\/978-981-99-1702-0"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1109\/JMEMS.2019.2912649","article-title":"Magnetomicrofluidic Platforms for Organizing Arrays of Single-Particles and Particle-Pairs","volume":"28","year":"2019","journal-title":"J. Microelectromech. Syst."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"7448","DOI":"10.1109\/JSEN.2024.3355770","article-title":"A High-Throughput Hybrid Electromicrofluidic Platform for Organizing Single-Cell Protein Secretion Profiling Assays","volume":"24","author":"Dashti","year":"2024","journal-title":"IEEE Sens. J."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"179","DOI":"10.3390\/mi2020179","article-title":"Microvalves and Micropumps for BioMEMS","volume":"2","author":"Au","year":"2011","journal-title":"Micromachines"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1063\/1.1629781","article-title":"Scaling properties of a low-actuation pressure microfluidic valve","volume":"95","author":"Studer","year":"2003","journal-title":"J. Appl. Phys."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1126\/science.1076996","article-title":"Microfluidic large-scale integration","volume":"298","author":"Thorsen","year":"2002","journal-title":"Science"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ac0519460","article-title":"Microfluidic single-cell mRNA isolation and analysis","volume":"78","author":"Marcus","year":"2006","journal-title":"Anal. Chem."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Jain, A., Stavrakis, S., and deMello, A. (2024). Droplet-based microfluidics and enzyme evolution. Curr. Opin. Biotechnol., 87.","DOI":"10.1016\/j.copbio.2024.103097"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1039\/D3LC00729D","article-title":"Development and future of droplet microfluidics","volume":"24","author":"Nan","year":"2024","journal-title":"Lab. Chip"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e92","DOI":"10.1002\/dro2.92","article-title":"Recent advances in droplet-based microfluidics in liquid biopsy for cancer diagnosis","volume":"3","author":"Shi","year":"2024","journal-title":"Droplet"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"110212","DOI":"10.1016\/j.jfoodeng.2020.110212","article-title":"Microfluidic droplet formation in co-flow devices fabricated by micro 3D printing","volume":"290","author":"Zhang","year":"2021","journal-title":"J. Food Eng."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"3045","DOI":"10.1016\/j.ces.2004.04.006","article-title":"Drop formation in a co-flowing ambient fluid","volume":"59","author":"Cramer","year":"2004","journal-title":"Chem. Eng. Sci."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Yao, J., Lin, F., Kim, H.S., and Park, J. (2019). The Effect of Oil Viscosity on Droplet Generation Rate and Droplet Size in a T-Junction Microfluidic Droplet Generator. Micromachines, 10.","DOI":"10.3390\/mi10120808"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1007\/s10404-014-1348-4","article-title":"Y- and T-junction microfluidic devices: Effect of fluids and interface properties and operating conditions","volume":"17","author":"Ushikubo","year":"2014","journal-title":"Microfluid. Nanofluidics"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1039\/b510841a","article-title":"Formation of droplets and bubbles in a microfluidic T-junction\u2014Scaling and mechanism of break-up","volume":"6","author":"Garstecki","year":"2006","journal-title":"Lab. Chip"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Yin, Z., Huang, Z., Lin, X., Gao, X., and Bao, F. (2020). Droplet Generation in a Flow-Focusing Microfluidic Device with External Mechanical Vibration. Micromachines, 11.","DOI":"10.3390\/mi11080743"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"21616","DOI":"10.1038\/s41598-020-77836-y","article-title":"Microfluidic droplet generation based on non-embedded co-flow-focusing using 3D printed nozzle","volume":"10","author":"Dewandre","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/978-1-4939-9240-9_6","article-title":"Single-Cell RNA Sequencing with Drop-Seq","volume":"1979","author":"Bageritz","year":"2019","journal-title":"Methods Mol. Biol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2015.04.044","article-title":"Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells","volume":"161","author":"Klein","year":"2015","journal-title":"Cell"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/j.devcel.2020.04.009","article-title":"Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development","volume":"53","author":"Lu","year":"2020","journal-title":"Dev. Cell"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/nmeth.4179","article-title":"Seq-Well: Portable, low-cost RNA sequencing of single cells at high throughput","volume":"14","author":"Gierahn","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Ramskold, D., Luo, S., Wang, Y.C., Li, R., Deng, Q., Faridani, O.R., Daniels, G.A., Khrebtukova, I., Loring, J.F., and Laurent, L.C. (2020). Author Correction: Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol., 38.","DOI":"10.1038\/s41587-020-0427-1"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"e2113568118","DOI":"10.1073\/pnas.2113568118","article-title":"Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states","volume":"118","author":"Isakova","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nprot.2014.006","article-title":"Full-length RNA-seq from single cells using Smart-seq2","volume":"9","author":"Picelli","year":"2014","journal-title":"Nat. Protoc."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1038\/nmeth.2639","article-title":"Smart-seq2 for sensitive full-length transcriptome profiling in single cells","volume":"10","author":"Picelli","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/s41587-020-0497-0","article-title":"Single-cell RNA counting at allele and isoform resolution using Smart-seq3","volume":"38","author":"Ziegenhain","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1126\/science.aam8940","article-title":"Comprehensive single-cell transcriptional profiling of a multicellular organism","volume":"357","author":"Cao","year":"2017","journal-title":"Science"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nmeth.4145","article-title":"Effective detection of variation in single-cell transcriptomes using MATQ-seq","volume":"14","author":"Sheng","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.celrep.2012.08.003","article-title":"CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification","volume":"2","author":"Hashimshony","year":"2012","journal-title":"Cell Rep."},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Hashimshony, T., Senderovich, N., Avital, G., Klochendler, A., de Leeuw, Y., Anavy, L., Gennert, D., Li, S., Livak, K.J., and Rozenblatt-Rosen, O. (2016). CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol., 17.","DOI":"10.1186\/s13059-016-0938-8"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1038\/nbt.1495","article-title":"The potential and challenges of nanopore sequencing","volume":"26","author":"Branton","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1038\/s41587-021-00965-w","article-title":"Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq","volume":"39","author":"Philpott","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"4124","DOI":"10.1038\/s41467-023-39813-7","article-title":"High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors","volume":"14","author":"Shiau","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"34","DOI":"10.2174\/1872210510666160602152913","article-title":"Nanotechnology and Nanopore Sequencing","volume":"11","year":"2017","journal-title":"Recent. Pat. Nanotechnol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.1038\/s41587-021-01108-x","article-title":"Nanopore sequencing technology, bioinformatics and applications","volume":"39","author":"Wang","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"110662","DOI":"10.1016\/j.celrep.2022.110662","article-title":"Progenitor potential of lung epithelial organoid cells in a transplantation model","volume":"39","author":"Louie","year":"2022","journal-title":"Cell Rep."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1111\/dgd.12608","article-title":"Nanopore sequencing: Review of potential applications in functional genomics","volume":"61","author":"Kono","year":"2019","journal-title":"Dev. Growth Differ."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/s44161-022-00028-6","article-title":"Single-cell transcriptomics reveals cell-type-specific diversification in human heart failure","volume":"1","author":"Koenig","year":"2022","journal-title":"Nat. Cardiovasc. Res."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1161\/CIRCULATIONAHA.119.041433","article-title":"Single-Cell RNA Sequencing Unveils Unique Transcriptomic Signatures of Organ-Specific Endothelial Cells","volume":"142","author":"Paik","year":"2020","journal-title":"Circulation"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1161\/CIRCRESAHA.119.316470","article-title":"Impact of Local Alloimmunity and Recipient Cells in Transplant Arteriosclerosis","volume":"127","author":"Cai","year":"2020","journal-title":"Circ. Res."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1161\/CIRCULATIONAHA.121.057400","article-title":"Donor Macrophages Modulate Rejection after Heart Transplantation","volume":"146","author":"Kopecky","year":"2022","journal-title":"Circulation"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1161\/ATVBAHA.120.315373","article-title":"Single-Cell Transcriptomic Atlas of Different Human Cardiac Arteries Identifies Cell Types Associated with Vascular Physiology","volume":"41","author":"Hu","year":"2021","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"868466","DOI":"10.3389\/fcvm.2022.868466","article-title":"Cellular Heterogeneity of the Heart","volume":"9","author":"Bugger","year":"2022","journal-title":"Front. Cardiovasc. Med."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"110322","DOI":"10.1016\/j.ygeno.2022.110322","article-title":"Single cell study of cellular diversity and mutual communication in chronic heart failure and drug repositioning","volume":"114","author":"Wan","year":"2022","journal-title":"Genomics"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"6242","DOI":"10.7150\/thno.75543","article-title":"Single-Cell RNA sequencing reveals immune cell dynamics and local intercellular communication in acute murine cardiac allograft rejection","volume":"12","author":"Chen","year":"2022","journal-title":"Theranostics"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"2089","DOI":"10.1161\/CIRCULATIONAHA.119.041694","article-title":"Single-Cell Sequencing of Mouse Heart Immune Infiltrate in Pressure Overload\u2013Driven Heart Failure Reveals Extent of Immune Activation","volume":"140","author":"Martini","year":"2019","journal-title":"Circulation"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.healun.2022.10.017","article-title":"The dynamic cellular landscape of grafts with acute rejection after heart transplantation","volume":"42","author":"Kong","year":"2023","journal-title":"J. Heart Lung Transplant."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4070\/kcj.2022.0295","article-title":"Strategy of Patient-Specific Therapeutics in Cardiovascular Disease through Single-Cell RNA Sequencing","volume":"53","author":"Jung","year":"2023","journal-title":"Korean Circ. J."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1161\/CIRCULATIONAHA.116.022907","article-title":"Gene Expression Profiling for the Identification and Classification of Antibody-Mediated Heart Rejection","volume":"135","author":"Loupy","year":"2017","journal-title":"Circulation"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1161\/CIRCULATIONAHA.119.043545","article-title":"Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis","volume":"142","author":"Hua","year":"2020","journal-title":"Circulation"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"102653","DOI":"10.1016\/j.jaut.2021.102653","article-title":"Transcriptome landscape of double negative T cells by single-cell RNA sequencing","volume":"121","author":"Yang","year":"2021","journal-title":"J. Autoimmun."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1161\/ATVBAHA.122.318333","article-title":"Multiomic Spatial Mapping of Myocardial Infarction and Implications for Personalized Therapy","volume":"43","author":"Schumacher","year":"2023","journal-title":"Arterioscler. Thromb. Vasc. Biol."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/s41581-019-0237-1","article-title":"The power of one: Advances in single-cell genomics in the kidney","volume":"16","author":"Clark","year":"2020","journal-title":"Nat. Rev. Nephrol."},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"19619","DOI":"10.1073\/pnas.1908706116","article-title":"The single-cell transcriptomic landscape of early human diabetic nephropathy","volume":"116","author":"Wilson","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1126\/science.aat1699","article-title":"Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors","volume":"361","author":"Young","year":"2018","journal-title":"Science"},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.1038\/s41467-021-22368-w","article-title":"Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney","volume":"12","author":"Muto","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"693608","DOI":"10.3389\/fimmu.2021.693608","article-title":"Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in Mice","volume":"12","author":"Shen","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"e170191","DOI":"10.1172\/JCI170191","article-title":"Single-cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality","volume":"133","author":"Shi","year":"2023","journal-title":"J. Clin. Investig."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1681\/ASN.2020030326","article-title":"Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant","volume":"31","author":"Malone","year":"2020","journal-title":"J. Am. Soc. Nephrol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"8851","DOI":"10.7150\/thno.48201","article-title":"Single-cell analysis reveals immune landscape in kidneys of patients with chronic transplant rejection","volume":"10","author":"Liu","year":"2020","journal-title":"Theranostics"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"706580","DOI":"10.3389\/fphar.2021.706580","article-title":"Single-Cell Transcriptomic Analysis of Peripheral Blood Reveals a Novel B-Cell Subset in Renal Allograft Recipients with Accommodation","volume":"12","author":"Zhuang","year":"2021","journal-title":"Front. Pharmacol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"4372","DOI":"10.1038\/s41467-021-24615-6","article-title":"Innate-like self-reactive B cells infiltrate human renal allografts during transplant rejection","volume":"12","author":"Asano","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"4359","DOI":"10.1038\/s41467-023-39859-7","article-title":"Transcriptional and spatial profiling of the kidney allograft unravels a central role for FcyRIII+ innate immune cells in rejection","volume":"14","author":"Lamarthee","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_117","doi-asserted-by":"crossref","unstructured":"van der List, A.C.J., Litjens, N.H.R., Brouwer, R.W.W., Klepper, M., den Dekker, A.T., van Ijcken, W.F.J., and Betjes, M.G.H. (2023). Single-Cell RNA Sequencing of Donor-Reactive T Cells Reveals Role of Apoptosis in Donor-Specific Hyporesponsiveness of Kidney Transplant Recipients. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241914463"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"e141321","DOI":"10.1172\/jci.insight.141321","article-title":"Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection","volume":"5","author":"Dangi","year":"2020","journal-title":"JCI Insight"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"5746832","DOI":"10.1155\/2020\/5746832","article-title":"Profiling the Resident and Infiltrating Monocyte\/Macrophages during Rejection following Kidney Transplantation","volume":"2020","author":"Wang","year":"2020","journal-title":"J. Immunol. Res."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"5462","DOI":"10.1038\/s41467-019-13382-0","article-title":"Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation","volume":"10","author":"Subramanian","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_121","doi-asserted-by":"crossref","unstructured":"Garreta, E., Nauryzgaliyeva, Z., and Montserrat, N. (2021). Human induced pluripotent stem cell-derived kidney organoids toward clinical implementations. Curr. Opin. Biomed. Eng., 20.","DOI":"10.1016\/j.cobme.2021.100346"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"e147703","DOI":"10.1172\/jci.insight.147703","article-title":"Integration of spatial and single-cell transcriptomics localizes epithelial cell-immune cross-talk in kidney injury","volume":"6","author":"Sabo","year":"2021","journal-title":"JCI Insight"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"108525","DOI":"10.1016\/j.celrep.2020.108525","article-title":"Single-Cell Transcriptomics Reveal Immune Mechanisms of the Onset and Progression of IgA Nephropathy","volume":"33","author":"Zheng","year":"2020","journal-title":"Cell Rep."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.2215\/CJN.14010820","article-title":"Urinary Cell mRNA Profiles Predictive of Human Kidney Allograft Status","volume":"16","author":"Lubetzky","year":"2021","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"1434","DOI":"10.1016\/j.ajt.2023.04.035","article-title":"Single-cell RNA sequencing reveals peripheral blood mononuclear immune cell landscape associated with operational tolerance in a kidney transplant recipient","volume":"23","author":"Azim","year":"2023","journal-title":"Am. J. Transplant."},{"key":"ref_126","first-page":"305","article-title":"Single Cell Rna-Sequencing of Urinary Cells and Defining the Immune Landscape of Rejection in Human Kidney Allografts","volume":"21","author":"Muthukumar","year":"2021","journal-title":"Am. J. Transplant"},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"767618","DOI":"10.3389\/fimmu.2021.767618","article-title":"Single-Cell Transcriptome Analysis of Chronic Antibody-Mediated Rejection after Renal Transplantation","volume":"12","author":"Kong","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_128","doi-asserted-by":"crossref","unstructured":"Wen, N., Wu, J., Li, H., Liao, J., Lan, L., Yang, X., Zhu, G., Lei, Z., Dong, J., and Sun, X. (2023). Immune landscape in rejection of renal transplantation revealed by high-throughput single-cell RNA sequencing. Front. Cell Dev. Biol., 11.","DOI":"10.3389\/fcell.2023.1208566"},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Suryawanshi, H., Yang, H., Lubetzky, M., Morozov, P., Lagman, M., Thareja, G., Alonso, A., Li, C., Snopkowski, C., and Belkadi, A. (2022). Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts. PLoS ONE, 17.","DOI":"10.1371\/journal.pone.0267704"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"e27865","DOI":"10.1016\/j.heliyon.2024.e27865","article-title":"Single-cell and bulk RNA sequencing highlights the role of M1-like infiltrating macrophages in antibody-mediated rejection after kidney transplantation","volume":"10","author":"Pang","year":"2024","journal-title":"Heliyon"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1126\/science.aar2131","article-title":"Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease","volume":"360","author":"Park","year":"2018","journal-title":"Science"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"dev181743","DOI":"10.1242\/dev.181743","article-title":"Correction: Single cell analysis of adult mouse skeletal muscle stem cells in homeostatic and regenerative conditions","volume":"146","author":"Juan","year":"2019","journal-title":"Development"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1038\/s41467-019-10291-0","article-title":"A comprehensive single cell transcriptional landscape of human hematopoietic progenitors","volume":"10","author":"Pellin","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"876","DOI":"10.1111\/ajt.16871","article-title":"Multiplexed droplet single-cell sequencing (Mux-Seq) of normal and transplant kidney","volume":"22","author":"Rashmi","year":"2022","journal-title":"Am. J. Transplant."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"S149","DOI":"10.1016\/j.healun.2021.01.454","article-title":"Deconvolution of Donor and Recipient Cells from Lung Transplant Single Cell RNA-seq Data","volume":"40","author":"Wilson","year":"2021","journal-title":"J. Heart Lung Transplant."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"e156648","DOI":"10.1172\/jci.insight.156648","article-title":"Single-cell transcriptome mapping identifies a local, innate B cell population driving chronic rejection after lung transplantation","volume":"7","author":"Smirnova","year":"2022","journal-title":"JCI Insight"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"eaav5581","DOI":"10.1126\/sciimmunol.aav5581","article-title":"Generation and persistence of human tissue-resident memory T cells in lung transplantation","volume":"4","author":"Snyder","year":"2019","journal-title":"Sci. Immunol."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"eabe4282","DOI":"10.1126\/scitranslmed.abe4282","article-title":"Lung transplantation for patients with severe COVID-19","volume":"12","author":"Bharat","year":"2020","journal-title":"Sci. Transl. Med."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"L1101","DOI":"10.1152\/ajplung.00089.2021","article-title":"Advanced single-cell technologies to guide the development of bioengineered lungs","volume":"320","author":"Wanczyk","year":"2021","journal-title":"Am. J. Physiol. Lung Cell. Mol. Physiol."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1016\/j.celrep.2014.04.011","article-title":"Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis","volume":"7","author":"Mahata","year":"2014","journal-title":"Cell Rep."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1038\/s41467-021-21865-2","article-title":"Single cell transcriptomic analysis of murine lung development on hyperoxia-induced damage","volume":"12","author":"Hurskainen","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_142","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"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"483","DOI":"10.2217\/bmm-2021-1013","article-title":"Markers of rejection of a lung allograft: State of the art","volume":"16","author":"Silva","year":"2022","journal-title":"Biomark. Med."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"2387","DOI":"10.1084\/jem.20162152","article-title":"Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span","volume":"214","author":"Misharin","year":"2017","journal-title":"J. Exp. Med."},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Lunardi, F., Abbrescia, D.I., Vedovelli, L., Pezzuto, F., Fortarezza, F., Comacchio, G.M., Guzzardo, V., Ferrigno, P., Loy, M., and Giraudo, C. (2023). Molecular Profiling of Tissue Samples with Chronic Rejection from Patients with Chronic Lung Allograft Dysfunction: A Pilot Study in Cystic Fibrosis Patients. Biomolecules, 13.","DOI":"10.3390\/biom13010097"},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.34067\/KID.0003842021","article-title":"Monocytes and Macrophages in Kidney Transplantation and Insights from Single Cell RNA-Seq Studies","volume":"2","author":"Malone","year":"2021","journal-title":"Kidney360"},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1016\/j.cell.2014.11.018","article-title":"Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment","volume":"159","author":"Lavin","year":"2014","journal-title":"Cell"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1164\/rccm.201712-2410OC","article-title":"Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis","volume":"199","author":"Reyfman","year":"2018","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_149","doi-asserted-by":"crossref","unstructured":"Snyder, M.E., Moghbeli, K., Bondonese, A., Craig, A., Popescu, I., Fan, L., Tabib, T., Lafyatis, R., Chen, K., and Trejo Bittar, H.E. (2021). Human lung tissue resident memory T cells are re-programmed but not eradicated with systemic glucocorticoids after acute cellular rejection. medRxiv.","DOI":"10.1101\/2021.09.27.21263985"},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/s11626-020-00433-w","article-title":"Concurrent isolation of hepatic stem cells and hepatocytes from the human liver","volume":"56","author":"Lee","year":"2020","journal-title":"In Vitro Cell Dev. Biol. Anim."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"106632","DOI":"10.1016\/j.intimp.2020.106632","article-title":"Isolation and purification of immune cells from the liver","volume":"85","author":"Shi","year":"2020","journal-title":"Int. Immunopharmacol."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"4383","DOI":"10.1038\/s41467-018-06318-7","article-title":"Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations","volume":"9","author":"MacParland","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1038\/s41419-021-03878-3","article-title":"Resolving the graft ischemia-reperfusion injury during liver transplantation at the single cell resolution","volume":"12","author":"Wang","year":"2021","journal-title":"Cell Death Dis."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"e13116","DOI":"10.1111\/cpr.13116","article-title":"Single-cell profiling reveals distinct immune phenotypes that contribute to ischaemia-reperfusion injury after steatotic liver transplantation","volume":"54","author":"Yang","year":"2021","journal-title":"Cell Prolif."},{"key":"ref_155","doi-asserted-by":"crossref","unstructured":"Wang, Z., Shao, X., Wang, K., Lu, X., Zhuang, L., Yang, X., Zhang, P., Yang, P., Zheng, S., and Xu, X. (2022). Single-cell analysis reveals a pathogenic cellular module associated with early allograft dysfunction after liver transplantation. bioRxiv.","DOI":"10.1101\/2022.02.09.479667"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1097\/TP.0000000000004365","article-title":"Decoding Single-cell Landscape and Intercellular Crosstalk in the Transplanted Liver","volume":"107","author":"Huang","year":"2023","journal-title":"Transplantation"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1002\/hep4.1930","article-title":"Single-cell transcriptomics reveals conserved cell identities and fibrogenic phenotypes in zebrafish and human liver","volume":"6","author":"Morrison","year":"2022","journal-title":"Hepatol. Commun."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"890019","DOI":"10.3389\/fimmu.2022.890019","article-title":"Landscape of immune cells heterogeneity in liver transplantation by single-cell RNA sequencing analysis","volume":"13","author":"Li","year":"2022","journal-title":"Front. Immunol."},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"1096733","DOI":"10.3389\/fimmu.2023.1096733","article-title":"Single-cell RNA-seq revealing the immune features of donor liver during liver transplantation","volume":"14","author":"Shan","year":"2023","journal-title":"Front. Immunol."},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"928256","DOI":"10.3389\/fgene.2022.928256","article-title":"Single-cell transcriptome sequencing reveals potential novel combination of biomarkers for antibody-based cancer therapeutics in hepatocellular carcinoma","volume":"13","author":"Tang","year":"2022","journal-title":"Front. Genet."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1038\/s41467-023-37674-8","article-title":"Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver","volume":"14","author":"Hautz","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1038\/s41421-020-0157-z","article-title":"Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human","volume":"6","author":"Zhao","year":"2020","journal-title":"Cell Discov."},{"key":"ref_163","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1038\/s41586-019-1631-3","article-title":"Resolving the fibrotic niche of human liver cirrhosis at single-cell level","volume":"575","author":"Ramachandran","year":"2019","journal-title":"Nature"},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41586-019-1373-2","article-title":"A human liver cell atlas reveals heterogeneity and epithelial progenitors","volume":"572","author":"Aizarani","year":"2019","journal-title":"Nature"},{"key":"ref_165","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1016\/j.cell.2019.10.003","article-title":"Landscape and dynamics of single immune cells in hepatocellular carcinoma","volume":"179","author":"Zhang","year":"2019","journal-title":"Cell"},{"key":"ref_166","first-page":"91","article-title":"Revisiting transplant immunology through the lens of single-cell technologies","volume":"45","author":"Barbetta","year":"2023","journal-title":"Semin. Immunopathol."},{"key":"ref_167","doi-asserted-by":"crossref","unstructured":"Roushansarai, N.S., Pascher, A., and Becker, F. (2022). Innate Immune Cells during Machine Perfusion of Liver Grafts\u2014The Janus Face of Hepatic Macrophages. J. Clin. Med., 11.","DOI":"10.3390\/jcm11226669"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.3389\/fimmu.2019.01036","article-title":"Chronic liver disease in humans causes expansion and differentiation of liver lymphatic endothelial cells","volume":"10","author":"Tamburini","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"1832","DOI":"10.1016\/j.celrep.2019.10.024","article-title":"Single-cell transcriptomics uncovers zonation of function in the mesenchyme during liver fibrosis","volume":"29","author":"Dobie","year":"2019","journal-title":"Cell Rep."},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"5380","DOI":"10.1172\/JCI137110","article-title":"Targeting tumor-associated macrophages and granulocytic myeloid-derived suppressor cells augments PD-1 blockade in cholangiocarcinoma","volume":"130","author":"Loeuillard","year":"2020","journal-title":"J. Clin. Investig."},{"key":"ref_171","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1002\/hep.32317","article-title":"TNF receptor\u2013related factor 3 inactivation promotes the development of intrahepatic cholangiocarcinoma through NF-\u03baB-inducing kinase\u2013mediated hepatocyte transdifferentiation","volume":"77","author":"Shiode","year":"2022","journal-title":"Hepatology"},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/s41698-020-0119-9","article-title":"Decreased cytotoxic T cells and TCR clonality in organ transplant recipients with squamous cell carcinoma","volume":"4","author":"Frazzette","year":"2020","journal-title":"NPJ Precis. Oncol."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"1748","DOI":"10.1056\/NEJMra1716145","article-title":"Stem Cells in the Treatment of Disease","volume":"380","author":"Blau","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref_174","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1038\/s41409-022-01631-8","article-title":"Impact of maintenance therapy post autologous stem cell transplantation for multiple myeloma in early and delayed transplant","volume":"57","author":"Karam","year":"2022","journal-title":"Bone Marrow Transplant."},{"key":"ref_175","doi-asserted-by":"crossref","first-page":"e66512","DOI":"10.7554\/eLife.66512","article-title":"External signals regulate continuous transcriptional states in hematopoietic stem cells","volume":"10","author":"Fast","year":"2021","journal-title":"Elife"},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"9483166","DOI":"10.1155\/2022\/9483166","article-title":"Single-Cell RNA Sequencing Reveals the Interaction of Injected ADSCs with Lung-Originated Cells in Mouse Pulmonary Fibrosis","volume":"2022","author":"Rahman","year":"2022","journal-title":"Stem Cells Int."},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"giz047","DOI":"10.1093\/gigascience\/giz047","article-title":"Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood","volume":"8","author":"Zhao","year":"2019","journal-title":"Gigascience"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"eabg5369","DOI":"10.1126\/sciadv.abg5369","article-title":"Single-cell architecture and functional requirement of alternative splicing during hematopoietic stem cell formation","volume":"8","author":"Wang","year":"2022","journal-title":"Sci. Adv."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1182\/blood-2021-150093","article-title":"Single-Cell Clonal Tracking in Allogeneic Hematopoietic Stem Cell Transplantation Reveals Time Dependent and Distinct Functional Patterns in Traceable Donor T Cell Clones","volume":"138","author":"Wittenbecher","year":"2021","journal-title":"Blood"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"108067","DOI":"10.1016\/j.celrep.2020.108067","article-title":"Single-cell transcriptome profiling reveals \u03b2 cell maturation in stem cell-derived islets after transplantation","volume":"32","author":"Augsornworawat","year":"2020","journal-title":"Cell Rep."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"2434","DOI":"10.1038\/s41467-020-16225-5","article-title":"Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson\u2019s disease","volume":"11","author":"Nolbrant","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.stemcr.2021.11.012","article-title":"Tubastatin A maintains adult skeletal muscle stem cells in a quiescent state ex vivo and improves their engraftment ability in vivo","volume":"17","author":"Arjona","year":"2022","journal-title":"Stem Cell Rep."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"2064","DOI":"10.1126\/science.1114758","article-title":"Direct isolation of satellite cells for skeletal muscle regeneration","volume":"309","author":"Montarras","year":"2005","journal-title":"Science"},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/s41556-020-0512-1","article-title":"Differentiation of transplanted haematopoietic stem cells tracked by single-cell transcriptomic analysis","volume":"22","author":"Dong","year":"2020","journal-title":"Nat. Cell Biol."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"eabe2634","DOI":"10.1126\/sciimmunol.abe2634","article-title":"Human skin-resident host T cells can persist long term after allogeneic stem cell transplantation and maintain recirculation potential","volume":"7","author":"Lichtner","year":"2022","journal-title":"Sci. Immunol."},{"key":"ref_186","doi-asserted-by":"crossref","unstructured":"Sun, C., Wang, H., Ma, Q., Chen, C., Yue, J., Li, B., and Zhang, X. (2021). Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells. Cell Biosci., 11.","DOI":"10.1186\/s13578-021-00541-4"},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"11075","DOI":"10.1038\/ncomms11075","article-title":"Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells","volume":"7","author":"Grover","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"eaax9106","DOI":"10.1126\/scitranslmed.aax9106","article-title":"Gene-edited human stem cell\u2013derived \u03b2 cells from a patient with monogenic diabetes reverse preexisting diabetes in mice","volume":"12","author":"Maxwell","year":"2020","journal-title":"Sci. Transl. Med."},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"105395","DOI":"10.1016\/j.isci.2022.105395","article-title":"Single-cell RNA sequencing reveals different signatures of mesenchymal stromal cell pluripotent-like and multipotent populations","volume":"25","author":"Oguma","year":"2022","journal-title":"iScience"},{"key":"ref_191","doi-asserted-by":"crossref","unstructured":"Cesaro, A., Defrene, J., Lachhab, A., Page, N., Tardif, M.R., Al-Shami, A., Oravecz, T., Fortin, P.R., Daudelin, J.F., and Labrecque, N. (2019). Enhanced myelopoiesis and aggravated arthritis in S100a8-deficient mice. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0221528"},{"key":"ref_192","doi-asserted-by":"crossref","first-page":"702636","DOI":"10.3389\/fimmu.2021.702636","article-title":"Exploiting Single-Cell Tools in Gene and Cell Therapy","volume":"12","author":"Bode","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/s41421-022-00417-y","article-title":"Decoding lymphomyeloid divergence and immune hyporesponsiveness in G-CSF-primed human bone marrow by single-cell RNA-seq","volume":"8","author":"You","year":"2022","journal-title":"Cell Discov."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"6410","DOI":"10.1038\/s41467-020-19917-0","article-title":"Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy","volume":"11","author":"Wisdom","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"5024","DOI":"10.1038\/s41467-021-25240-z","article-title":"Single-cell evaluation reveals shifts in the tumor-immune niches that shape and maintain aggressive lesions in the breast","volume":"12","author":"Sinha","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1126\/science.aad0501","article-title":"Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq","volume":"352","author":"Tirosh","year":"2016","journal-title":"Science"},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"1277","DOI":"10.1038\/s41591-018-0096-5","article-title":"Phenotype molding of stromal cells in the lung tumor microenvironment","volume":"24","author":"Lambrechts","year":"2018","journal-title":"Nat. Med."},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1038\/s41591-020-0844-1","article-title":"A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors","volume":"26","author":"Slyper","year":"2020","journal-title":"Nat. Med."},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"e20200853","DOI":"10.1084\/jem.20200853","article-title":"Autoimmunity affecting the biliary tract fuels the immunosurveillance of cholangiocarcinoma","volume":"218","author":"Paillet","year":"2021","journal-title":"J. Exp. Med."},{"key":"ref_200","first-page":"8624963","article-title":"The Application of Single-Cell RNA Sequencing in Vaccinology","volume":"2020","author":"Cargill","year":"2020","journal-title":"J. Immunol. Res."}],"container-title":["Biosensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6374\/14\/4\/189\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T14:26:07Z","timestamp":1760106367000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6374\/14\/4\/189"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,11]]},"references-count":200,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2024,4]]}},"alternative-id":["bios14040189"],"URL":"https:\/\/doi.org\/10.3390\/bios14040189","relation":{},"ISSN":["2079-6374"],"issn-type":[{"value":"2079-6374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,11]]}}}