Automated high-throughput profiling of single-cell total transcriptome with scComplete-seq

Detecting the complete transcriptome, including polyadenylated and nonpolyadenylated RNA, is crucial for understanding cellular roles. However, current efforts to investigate the total cellular transcriptome in single cells are limited by the lack of an automated, high-throughput assay. We developed scComplete-seq, a method that enhances existing droplet-based single-cell mRNA sequencing to provide insights into the nonpolyadenylated transcriptome. This method allows us to detect long and short nonpolyadenylated RNAs at single-cell resolution, including histone RNAs and enhancer RNAs in cancer cells and peripheral blood mononuclear cells (PBMCs). Using scComplete-seq, we identified transcriptomic changes in PBMCs under various stimulations, revealing specific biological processes and associated enhancer activities.