SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression

Area of Science:

• Biomedical Sciences
• Genomics
• Molecular Biology

Background:

• Single-cell mRNA sequencing (RNA-seq) is crucial for understanding cellular heterogeneity.
• Existing methods face challenges in quantitative accuracy and cost-effectiveness.

Purpose of the Study:

• To introduce single-cell mRNA 3-prime end sequencing (SC3-seq), a novel, quantitative, and cost-effective methodology.
• To demonstrate the utility of SC3-seq for analyzing gene expression at single-cell resolution.

Main Methods:

• SC3-seq utilizes PCR amplification and 3-prime-end enrichment for gene expression measurement.
• Quantitative accuracy is achieved by regressing read counts of spike-in RNAs with defined copy numbers.
• The method allows for high sequence depth for comprehensive transcript detection.

Main Results:

• SC3-seq provides highly quantitative mRNA measurements from single cells to 10,000-cell levels.
• The method accurately estimates transcript levels, outperforming other single-cell RNA-seq techniques.
• SC3-seq successfully identified four distinct cell types in mouse blastocysts and revealed heterogeneity in human-induced pluripotent stem cells (hiPSCs).

Conclusions:

• SC3-seq offers significant advantages for quantitative transcript analysis in single cells.
• The method demonstrates high sensitivity and accuracy for transcriptome profiling.
• SC3-seq is proposed as a powerful tool for broad applications in biomedical research, including stem cell biology and developmental studies.