Protocol for single-cell ATAC sequencing using combinatorial indexing in mouse lung adenocarcinoma

Area of Science:

• Genomics
• Molecular Biology
• Epigenetics

Background:

• Chromatin accessibility profiling is crucial for understanding gene regulation.
• Single-cell resolution provides insights into cellular heterogeneity.
• Existing methods like droplet-based ATAC-seq have limitations in cost and scalability.

Purpose of the Study:

• To describe a detailed protocol for single-cell ATAC sequencing using combinatorial indexing (sciATAC-seq).
• To highlight the advantages of sciATAC-seq, including cost-effectiveness and flexibility.
• To present sciATAC-seq as a viable alternative to commercial droplet-based methods.

Main Methods:

• Utilizes a dual-barcoding strategy during transposition and library construction.
• Employs combinatorial indexing for multiplexing across samples or perturbations.
• The protocol is designed for diverse cell types and fixed samples.

Main Results:

• Achieves single-cell resolution of chromatin accessibility profiles.
• Demonstrates cost-effectiveness and extensibility compared to droplet-based methods.
• Provides a flexible experimental scale through multiplexed barcoding.

Conclusions:

• sciATAC-seq is a powerful, cost-effective, and flexible tool for single-cell chromatin accessibility studies.
• The protocol is adaptable to various biological samples and experimental scales.
• Offers a valuable alternative for researchers seeking scalable and economical ATAC-seq solutions.