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Updated: Jan 11, 2026
Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
Published on: February 1, 2022
A drop-based workflow for fast and robust joint profiling of transcriptome and chromatin accessibility in the same
Ziying Yang1,2, Siqi Liu1,2, Changya Chen1,2
1State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
We developed a high-throughput droplet-based microfluidic protocol for simultaneous single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq). This method links gene expression and chromatin accessibility in individual cells, enhancing rare cell population identification.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- Single-cell multiomics advances understanding of cellular heterogeneity.
- Joint profiling of scRNA-seq and scATAC-seq links gene expression to chromatin accessibility.
- This integration improves identification of rare cell populations and epigenetic mechanisms.
Purpose of the Study:
- To present a robust, high-throughput droplet-based microfluidic protocol for simultaneous scRNA-seq and scATAC-seq.
- To enable direct linkage between gene expression and chromatin accessibility at single-cell resolution.
- To offer a scalable and reproducible method for dissecting complex biological systems.
Main Methods:
- Developed a droplet-based microfluidic protocol for simultaneous RNA and chromatin accessibility profiling.
- Streamlined workflow includes cell pretreatment, nuclei isolation, and GEM generation.
- Constructed scRNA-seq and scATAC-seq libraries for parallel processing of tens of thousands of cells.
Main Results:
- Achieved simultaneous profiling of RNA and chromatin accessibility from individual cells.
- Protocol demonstrated high-throughput capability, scalability, and reproducibility.
- Enabled integrative analysis of multiple features from the same cell.
Conclusions:
- The multimodal approach is invaluable for dissecting complex biological systems.
- This protocol enhances sensitivity and specificity in identifying rare cell populations.
- Facilitates elucidation of epigenetic regulatory mechanisms at single-cell resolution.
