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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
Published on: January 10, 2019
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SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics
Grant Kinsler1, Caitlin Fagan2, Haiyin Li3
1Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA. grantkinsler@gmail.com.
Nature Methods
|December 18, 2025
Summary
SpaceBar enables simultaneous clone tracing and spatial gene expression profiling. This new method distinguishes clonal dynamics from environmental influences in complex tissues.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- Imaging-based spatial transcriptomics measures spatial determinants of cellular phenotypes.
- Current methods are incompatible with clone-tracing, hindering simultaneous analysis of clonal and spatial drivers.
Purpose of the Study:
- To develop a method for simultaneous clone tracing and spatial gene expression profiling.
- To enable the study of both clonal dynamics and spatial influences on gene expression within complex tissues.
Main Methods:
- Developed SpaceBar, a system using a library of 96 synthetic barcode sequences.
- Combinatorially labels each cell with unique barcodes.
- Integrates with standard imaging-based spatial transcriptomics pipelines.
Main Results:
- SpaceBar allows simultaneous detection of clonal and spatial drivers.
- Successfully distinguishes between clonal dynamics and environmentally driven transcriptional regulation.
- Applicable to complex tissue contexts.
Conclusions:
- SpaceBar overcomes limitations of existing methods for combined clonal and spatial analysis.
- Provides a powerful tool for dissecting cellular behavior in complex biological systems.
- Facilitates a deeper understanding of tissue development and disease.
