Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte...

Area of Science:

• Genomics
• Cell Biology
• Biotechnology

Background:

• A human cell atlas is crucial for understanding biology and disease.
• High-throughput single-cell RNA sequencing (scRNA-seq) is powerful but limited by tissue accessibility.
• Single-nucleus RNA sequencing (snRNA-seq) offers an alternative for tissues where cell isolation is difficult.

Purpose of the Study:

• To compare the efficacy of Drop-seq (scRNA-seq) and DroNc-seq (snRNA-seq).
• To evaluate DroNc-seq for profiling heterogeneous postmortem human heart tissue.
• To assess the potential of snRNA-seq for generating human cell atlas reference maps.

Main Methods:

• Comparative analysis of Drop-seq and DroNc-seq using human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes.
• Time-course transcriptomic profiling of cellular and nuclear RNA.
• Application of DroNc-seq to postmortem human heart tissue.

Main Results:

• Both Drop-seq and DroNc-seq identified six distinct cell types during cardiomyocyte differentiation, with five common to both.
• Reconstructed single-cell trajectories accurately reflected expected differentiation dynamics.
• DroNc-seq demonstrated comparable performance to Drop-seq and suitability for heterogeneous human tissue.

Conclusions:

• DroNc-seq is a viable alternative to scRNA-seq for tissues with isolation challenges.
• snRNA-seq can successfully generate reference transcriptomic data for human tissue atlases.
• This study validates DroNc-seq for comprehensive cell type mapping in complex biological systems.