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bioRxiv · 10.1101/2024.03.12.584729

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

Dincaslan, F. B.·Ngang, S. W. Y.·Tan, R. Z.·Cheow, L. F.
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Abstract

Detecting the complete portrait of the transcriptome is essential to understanding the roles of both polyadenylated and non-polyadenylated RNA species. However, current efforts to investigate the heterogeneity of the total cellular transcriptome in single cells are limited by the lack of an automated, high-throughput assay that can be carried out on existing platforms. To address this issue, we developed scComplete-seq, a method that can easily augment existing high-throughput droplet-based single-cell mRNA sequencing to provide additional information on the non-polyadenylated transcriptome. Using scComplete-seq, we have successfully detected long and short non-polyadenylated RNAs at single-cell resolution, including cell-cycle-specific histone RNAs, cell-type-specific short non-coding RNA, as well as enhancer RNAs in cancer cells and PBMCs. By applying scComplete-seq, we have identified changes in both coding and non-coding transcriptome in PBMCs during different stimulations. Measuring the enhancer RNA expression also revealed the activation of specific biological processes and the transcription factors regulating such changes.

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Dincaslan, F. B., Ngang, S. W. Y., Tan, R. Z., Cheow, L. F.. 2024-03-14. Automated high-throughput profiling of single-cell total transcriptome with scComplete-seq. https://doi.org/10.1101/2024.03.12.584729

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