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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
Published on: January 10, 2019
sc-rDSeq: Droplet-based single-cell full-length total RNA-seq method
1Department of Biochemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
Biology Methods & Protocols
|June 19, 2026
Summary
sc‑rDSeq is a new single-cell RNA sequencing method that captures all RNA types, including non-polyadenylated RNAs. This provides a deeper understanding of cellular function and heterogeneity.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Conventional RNA sequencing often misses non-polyadenylated RNAs, limiting the view of cellular heterogeneity.
- Existing full-length RNA sequencing methods can be costly and complex.
Purpose of the Study:
- To introduce sc‑rDSeq, a scalable, droplet-based method for full-length, strand-specific total RNA sequencing at single-cell resolution.
- To enable comprehensive analysis of gene expression, alternative splicing, and single nucleotide variations.
Main Methods:
- Utilizes 220 refined ribosomal-depleted sequences (rDS) primers for selective rRNA exclusion during reverse transcription.
- Employs a single-step microfluidic workflow compatible with standard inDrops platforms.
- Includes sc‑rDSeq barcode synthesis, single-cell co-encapsulation, and library construction.
Main Results:
- Captures both polyadenylated and non-polyadenylated RNAs (e.g., histone, noncoding, enhancer RNAs).
- Achieves a 10-fold increase in unique molecular identifiers per cell compared to 3' end-based methods.
- Offers a reagent cost of approximately $0.08 per cell.
Conclusions:
- sc‑rDSeq provides a simpler, cost-effective, and more comprehensive approach to single-cell total RNA sequencing.
- Enables deeper insights into cellular regulatory programs and heterogeneity.
- Makes deep total transcriptome analysis more accessible to researchers.
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