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Updated: Apr 12, 2026
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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
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Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A Cusanovich1, Riza Daza1, Andrew Adey2
1University of Washington, Department of Genome Sciences, Seattle, WA, USA.
Science (New York, N.Y.)
|May 9, 2015
Summary
This study introduces a scalable method for epigenome profiling in thousands of single cells, overcoming previous limitations. The new technique enables detailed chromatin accessibility mapping to advance cell atlas projects.
Area of Science:
- Genomics
- Epigenetics
- Single-cell analysis
Background:
- Single-cell resolution genomics and transcriptomics are advanced.
- Single-cell epigenome characterization remains a challenge.
- Conventional methods for single-cell preparation have limitations in scalability.
Purpose of the Study:
- To develop a scalable method for single-cell epigenome profiling.
- To overcome the limitations of conventional single-cell preparation techniques.
- To enable large-scale chromatin accessibility analysis in single cells.
Main Methods:
- Applied combinatorial cellular indexing to measure chromatin accessibility.
- Avoided physical separation and compartmentalization of individual cells.
- Analyzed chromatin accessibility profiles from over 15,000 single cells.
Main Results:
- Successfully profiled chromatin accessibility in thousands of single cells per assay.
- Clustered cells based on chromatin accessibility landscapes.
- Identified modules of coordinated chromatin accessibility within and between cell types.
Conclusions:
- The developed method is scalable for epigenome profiling.
- This approach can accelerate the creation of a comprehensive human cell atlas.
- Enables detailed analysis of chromatin accessibility at the single-cell level.
