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Updated: Jun 20, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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.

Xue Sun¹, Oren Ram¹

¹Department of Biochemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.

Biology Methods & Protocols

|June 19, 2026

Summary

This summary is machine-generated.

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.

Keywords:

Drop-based microfluidics Full transcriptomics Single-cell total RNA-seq

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AQRNA-seq for Quantifying Small RNAs

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

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Last Updated: Jun 20, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

AQRNA-seq for Quantifying Small RNAs

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

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.