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Updated: Jan 8, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

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.

|December 18, 2025

Summary

This summary is machine-generated.

SpaceBar enables simultaneous clone tracing and spatial gene expression profiling. This new method distinguishes clonal dynamics from environmental influences in complex tissues.

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Last Updated: Jan 8, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

An Approach to Study Shape-Dependent Transcriptomics at a Single Cell Level

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Cell Lineage Analyses and Gene Function Studies Using Twin-spot MARCM

Cell Lineage Analyses and Gene Function Studies Using Twin-spot MARCM

Published on: March 2, 2017

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.