Nature Communications (Jul 2023)
Guided construction of single cell reference for human and mouse lung
- Minzhe Guo,
- Michael P. Morley,
- Cheng Jiang,
- Yixin Wu,
- Guangyuan Li,
- Yina Du,
- Shuyang Zhao,
- Andrew Wagner,
- Adnan Cihan Cakar,
- Michal Kouril,
- Kang Jin,
- Nathan Gaddis,
- Joseph A. Kitzmiller,
- Kathleen Stewart,
- Maria C. Basil,
- Susan M. Lin,
- Yun Ying,
- Apoorva Babu,
- Kathryn A. Wikenheiser-Brokamp,
- Kyu Shik Mun,
- Anjaparavanda P. Naren,
- Geremy Clair,
- Joshua N. Adkins,
- Gloria S. Pryhuber,
- Ravi S. Misra,
- Bruce J. Aronow,
- Timothy L. Tickle,
- Nathan Salomonis,
- Xin Sun,
- Edward E. Morrisey,
- Jeffrey A. Whitsett,
- NHLBI LungMAP Consortium,
- Yan Xu
Affiliations
- Minzhe Guo
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Michael P. Morley
- Department of Medicine, University of Pennsylvania
- Cheng Jiang
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Yixin Wu
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center
- Yina Du
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Shuyang Zhao
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Andrew Wagner
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Adnan Cihan Cakar
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center
- Kang Jin
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center
- Nathan Gaddis
- RTI International
- Joseph A. Kitzmiller
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Kathleen Stewart
- Department of Medicine, University of Pennsylvania
- Maria C. Basil
- Department of Medicine, University of Pennsylvania
- Susan M. Lin
- Department of Medicine, University of Pennsylvania
- Yun Ying
- Department of Medicine, University of Pennsylvania
- Apoorva Babu
- Department of Medicine, University of Pennsylvania
- Kathryn A. Wikenheiser-Brokamp
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Kyu Shik Mun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center
- Anjaparavanda P. Naren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center
- Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory
- Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory
- Gloria S. Pryhuber
- Department of Pediatrics Division of Neonatology, University of Rochester Medical Center
- Ravi S. Misra
- Department of Pediatrics Division of Neonatology, University of Rochester Medical Center
- Bruce J. Aronow
- Department of Pediatrics, University of Cincinnati College of Medicine
- Timothy L. Tickle
- Data Sciences Platform, The Broad Institute
- Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine
- Xin Sun
- Department of Pediatrics, University of California at San Diego
- Edward E. Morrisey
- Department of Medicine, University of Pennsylvania
- Jeffrey A. Whitsett
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- NHLBI LungMAP Consortium
- Yan Xu
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- DOI
- https://doi.org/10.1038/s41467-023-40173-5
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 20
Abstract
Abstract Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs.
