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Mouse Embryonic Lung Culture, A System to Evaluate the Molecular Mechanisms of Branching
Published on: June 30, 2010
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Guided construction of single cell reference for human and mouse lung.
Minzhe Guo1,2, Michael P Morley3,4,5, Cheng Jiang6
1The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA. minzhe.guo@cchmc.org.
Nature Communications
|July 29, 2023
Summary
Researchers created a LungMAP single-cell reference (CellRef) using lung transcriptomic data. This resource accurately annotates human and mouse lung cell types, aiding single-cell analysis and data sharing.
Area of Science:
- Single-cell genomics
- Computational biology
- Lung biology
Background:
- Accurate cell type identification is crucial for single-cell data analysis, but standardized references are lacking.
- Existing single-cell references often lack comprehensive cell types, functional validation, and common nomenclature.
- Automated cell type annotation, data integration, and sharing require robust, validated cell atlases.
Purpose of the Study:
- To construct a unified single-cell reference for normal human and mouse lungs.
- To provide a validated resource for automated cell type annotation and data integration.
- To develop accessible tools for researchers studying lung biology.
Main Methods:
- Developed a computational pipeline using LungMAP CellCards as a reference dictionary.
- Consolidated transcriptomic data from 104 human and 17 mouse lung samples.
- Defined and catalogued distinct lung cell types from various anatomical locations and developmental stages.
Main Results:
- Constructed the LungMAP single-cell reference (CellRef) defining 48 human and 40 mouse lung cell types.
- Demonstrated the accuracy and stability of CellRefs using independent datasets and multiple annotation methods.
- Validated the utility of CellRefs for automated cell type annotation in normal and diseased lung samples.
Conclusions:
- LungMAP CellRefs provide a validated, comprehensive resource for human and mouse lung cell type annotation.
- The developed CellRefs facilitate automated analysis, data integration, and sharing in lung single-cell research.
- User-friendly web interfaces enhance accessibility and utilization of the LungMAP CellRefs for the research community.
