biostudies-literatureDincaslan FBNational University of SingaporeNational Research Foundation Frontier Competitive Research ProgrammeSingapore Ministry of Education Tier 2 Academic Research Fund and National Research Foundation Frontier Competitive Research ProgramSingapore Ministry of Education Academic Research Fund Tier 2Institute for Health Innovation and Technologygkaf699https://www.ebi.ac.uk/biostudies/studies/S-EPMC12276002biostudies-literatureUnknown53(14)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 assocNucleic acids researchAutomated high-throughput profiling of single-cell total transcriptome with scComplete-seq.PMC12276002NRF-F-CRP-2024-0003MOE-T2EP30224-0020Cheow LFTan RZDincaslan FBNgang SWYfalseAutomated 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 assoc2025-01-01T00:00:00Z2025 Jul2025-08-27T03:06:36.606Z2025-08-21T09:53:08.737ZS-EPMC122760024068282710.1093/nar/gkaf699