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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: Nov 6, 2025

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

Experimental design for single-cell RNA sequencing.

Jeanette Baran-Gale¹, Tamir Chandra¹, Kristina Kirschner²

¹The Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK.

Briefings in Functional Genomics

|November 11, 2017

Summary

This summary is machine-generated.

Single-cell RNA sequencing (scRNA-seq) enables cellular heterogeneity studies. This review compares Smart-Seq2 and 10x Chromium microdroplet methods, guiding experimental design for successful scRNA-seq research.

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Last Updated: Nov 6, 2025

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

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Area of Science:

Genomics
Molecular Biology
Biotechnology

Background:

Single-cell RNA sequencing (scRNA-seq) is a powerful technique for analyzing cellular heterogeneity.
The field is rapidly advancing, necessitating clear experimental design guidelines.
Understanding different scRNA-seq approaches is crucial for researchers.

Purpose of the Study:

To provide an overview of experimental design considerations for scRNA-seq.
To compare two prominent scRNA-seq methodologies: plate-based Smart-Seq2 and microdroplet-based 10x Chromium.
To highlight the advantages and disadvantages of each method to aid researchers in selecting the optimal approach.

Main Methods:

Discussion of general experimental design principles for scRNA-seq.
Comparative analysis of Smart-Seq2 (plate-based) and 10x Chromium (microdroplet-based) platforms.
Evaluation of key factors influencing the success of scRNA-seq experiments.

Main Results:

Smart-Seq2 offers high sensitivity and full-length transcript coverage, suitable for in-depth analysis of smaller cell numbers.
10x Chromium enables high-throughput analysis of thousands of cells, ideal for capturing broad cellular heterogeneity.
Both methods have distinct advantages and limitations impacting data quality, cost, and experimental scope.

Conclusions:

The choice between Smart-Seq2 and 10x Chromium depends on specific research questions, cell type, and desired throughput.
Careful consideration of experimental design factors is paramount for obtaining reliable and meaningful scRNA-seq data.
This review provides essential insights for researchers navigating the evolving landscape of single-cell genomics.