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Updated: Aug 15, 2025

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

Benchmarking full-length transcript single cell mRNA sequencing protocols.

Victoria Probst¹, Arman Simonyan¹, Felix Pacheco¹

¹Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.

|December 29, 2022

Summary

This summary is machine-generated.

Plate-based single-cell RNA sequencing (scRNA-seq) protocols were evaluated for gene detection sensitivity and cost. Genome & Transcriptome sequencing (G&T) and SMART-seq3 (SS3) offer high performance at lower costs for high-throughput labs.

Keywords:

Benchmarking Full-length RNAseq G&T sequencing NEB SMART-seq3 Single cell Takara mRNA sequencing technologies

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Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Published on: October 27, 2011

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Last Updated: Aug 15, 2025

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Single Read and Paired End mRNA-Seq Illumina Libraries from 10 Nanograms Total RNA

Published on: October 27, 2011

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Single-cell mRNA sequencing (scRNA-seq) technologies have revolutionized the study of cellular heterogeneity and identity.
Plate-based scRNA-seq protocols are essential for applications requiring high transcript capture per cell, such as clinical marker estimation.

Purpose of the Study:

To evaluate the performance of four plate-based scRNA-seq protocols.
To compare gene detection sensitivity, reproducibility, cost, and hands-on time for clinical applications.

Main Methods:

Performance evaluation of four plate-based scRNA-seq protocols: NEBNext® Single Cell/ Low Input RNA Library Prep Kit (NEB®), SMART-seq® HT kit (Takara®), Genome & Transcriptome sequencing (G&T), and SMART-seq3 (SS3).
Assessment focused on high gene detection sensitivity, inter-sample reproducibility, and hands-on time.

Main Results:

Genome & Transcriptome sequencing (G&T) demonstrated the highest gene detection per single cell.
SMART-seq3 (SS3) offered the highest gene detection per single cell at the lowest cost.
The Takara® kit provided high gene detection and reproducibility but at the highest price, while NEB® offered lower gene detection but was a more affordable commercial option.

Conclusions:

Ease-of-use in scRNA-seq protocols often correlates with higher costs.
For analyzing a few samples where ease-of-use is paramount, the Takara® kit is suitable.
For laboratories with substantial sample throughput, the cost-effective G&T-seq or SS3 protocols are recommended.