MuMu: a sample multiplexing protocol for droplet-based simultaneous single nuclei RNA- and ATAC-seq systems.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Sample multiplexing is crucial for reducing costs and batch effects in high-throughput biological experiments.
• Simultaneous single-cell RNA sequencing (scRNA-seq) and ATAC sequencing (scATAC-seq) provide comprehensive multiomic insights.
• Existing protocols for multiomic analysis can be expensive and labor-intensive, limiting accessibility.

Purpose of the Study:

• To introduce a novel protocol for multiplexed single-cell multiomic analysis.
• To enable the pooling of single nuclei from diverse biological samples prior to multiomic profiling.
• To reduce the overall cost and technical burden associated with single-nucleus multiomic experiments.

Main Methods:

• Development of a custom Tn5 transposome for efficient transposition.
• Integration of nuclei pooling with simultaneous single-nucleus RNA sequencing (snRNA-seq) and single-nucleus ATAC sequencing (snATAC-seq).
• Detailed description of library preparation, sequencing, and data pre-processing steps for the Multiplexed Multiome (MuMu) protocol.

Main Results:

• Successful implementation of a protocol allowing pooled single nuclei from multiple samples for simultaneous snRNA-seq and snATAC-seq.
• Demonstration of key steps including custom transposome assembly, transposition reaction, nuclei pooling, and library preparation.
• The Multiplexed Multiome (MuMu) protocol significantly reduces the cost of sn-Multiome experiments.

Conclusions:

• The Multiplexed Multiome (MuMu) protocol offers a streamlined and cost-effective approach for simultaneous snRNA-seq and snATAC-seq.
• This method facilitates large-scale multiomic studies by lowering experimental barriers.
• MuMu is poised to enhance the accessibility and efficiency of single-cell multiomic analyses across various research fields.