Single-cell connectomic analysis of adult mammalian lungs
Abstract
INTRODUCTION
RESULTS
Single-cell profiling of lung creates a cross-species pulmonary atlas
Comparative ligand-receptor connectomics identifies conserved patterns of extracellular signaling
Recipient cell–specific networks illustrate niche character
Network mapping and gene-level findings support stereotyped cellular roles
ATI cells dominate the semaphorin and VEGF alveolar signaling across species
Alveolar network analysis identifies signaling modalities dominated by specific cell types
DISCUSSION
Summary
Drawbacks and limitations
Conclusion
MATERIALS AND METHODS
Experimental design
Cell dissociation (Yale)
Cell dissociation (Brigham and Women’s Hospital)
10× library preparation, sequencing, and alignment
Data filtration, normalization, and scaling
Summary statistics
Clustering
Integration of human samples across dissociation methods
Marker determination
Homolog conversion
Jaccard index plots
Human Protein Atlas mapping
Immunostaining and imaging
Connectome definition
Weight definition
Node definition
Global network analysis
Definition of species-conserved connectome
Distal niche definition and hive plot generation
Network centrality analysis
Online resource
Software
Statistical analysis
Acknowledgments
Supplementary Material
Summary
Resources
REFERENCES AND NOTES
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Published In
December 2019
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- Micha Sam Brickman Raredon et al.
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