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 and Yan Xu ()
Additional contact information
Minzhe Guo: Cincinnati Children’s Hospital Medical Center
Michael P. Morley: University of Pennsylvania
Cheng Jiang: Cincinnati Children’s Hospital Medical Center
Yixin Wu: Cincinnati Children’s Hospital Medical Center
Guangyuan Li: Cincinnati Children’s Hospital Medical Center
Yina Du: Cincinnati Children’s Hospital Medical Center
Shuyang Zhao: Cincinnati Children’s Hospital Medical Center
Andrew Wagner: Cincinnati Children’s Hospital Medical Center
Adnan Cihan Cakar: Cincinnati Children’s Hospital Medical Center
Michal Kouril: Cincinnati Children’s Hospital Medical Center
Kang Jin: Cincinnati Children’s Hospital Medical Center
Nathan Gaddis: RTI International
Joseph A. Kitzmiller: Cincinnati Children’s Hospital Medical Center
Kathleen Stewart: University of Pennsylvania
Maria C. Basil: University of Pennsylvania
Susan M. Lin: University of Pennsylvania
Yun Ying: University of Pennsylvania
Apoorva Babu: University of Pennsylvania
Kathryn A. Wikenheiser-Brokamp: Cincinnati Children’s Hospital Medical Center
Kyu Shik Mun: Cedars-Sinai Medical Center
Anjaparavanda P. Naren: Cedars-Sinai Medical Center
Geremy Clair: Pacific Northwest National Laboratory
Joshua N. Adkins: Pacific Northwest National Laboratory
Gloria S. Pryhuber: University of Rochester Medical Center
Ravi S. Misra: University of Rochester Medical Center
Bruce J. Aronow: University of Cincinnati College of Medicine
Timothy L. Tickle: The Broad Institute
Nathan Salomonis: University of Cincinnati College of Medicine
Xin Sun: University of California at San Diego
Edward E. Morrisey: University of Pennsylvania
Jeffrey A. Whitsett: Cincinnati Children’s Hospital Medical Center
Yan Xu: Cincinnati Children’s Hospital Medical Center

Nature Communications, 2023, vol. 14, issue 1, 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.

Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40173-5

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DOI: 10.1038/s41467-023-40173-5

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