Multiplexed single-cell RNA-sequencing of mouse thymic and splenic samples

Area of Science:

• Immunology
• Genomics
• Molecular Biology

Background:

• Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying cellular heterogeneity.
• Analyzing multiple samples in a single scRNA-seq experiment presents challenges, including cost and batch effects.

Purpose of the Study:

• To present a multiplexed scRNA-seq protocol using antibody-hashtag oligonucleotides (Ab-HTO) for simultaneous analysis of multiple samples.
• To demonstrate the application of this protocol for studying mouse thymocyte and splenic T lymphocyte development.

Main Methods:

• Multiplexing of biological samples using Ab-HTO for sample identification.
• 10x Genomics technology for high-throughput single-cell gene expression analysis.
• Application of the protocol to mouse thymocytes and splenic T lymphocytes.

Main Results:

• Successful multiplexing of samples, enabling cost reduction and batch effect mitigation.
• Effective analysis of gene expression profiles for mouse thymocyte and splenic T lymphocyte populations.
• Demonstrated utility of Ab-HTO for cell-doublet removal and merging of scRNA-seq datasets.

Conclusions:

• Multiplexed scRNA-seq with Ab-HTO is a cost-effective and robust method for analyzing multiple samples.
• This approach facilitates deeper insights into developmental processes, such as T lymphocyte maturation.
• The protocol provides a valuable tool for researchers in immunology and genomics.