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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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Related Experiment Video

Updated: Sep 6, 2025

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Published on: October 26, 2018

High-throughput total RNA sequencing in single cells using VASA-seq.

Fredrik Salmen^1,2, Joachim De Jonghe^3,4, Tomasz S Kaminski^3,5

¹Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, Netherlands.

Nature Biotechnology

|June 27, 2022

Summary

This summary is machine-generated.

VASA-seq captures the entire single-cell transcriptome, revealing new cell markers and improving analysis of RNA splicing and cell cycle dynamics in developing mouse embryos.

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Related Experiment Videos

Last Updated: Sep 6, 2025

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing DIVA-Seq

Published on: October 26, 2018

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

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

Area of Science:

Single-cell genomics
Transcriptomics
Developmental biology

Background:

Current single-cell RNA sequencing methods capture only polyadenylated transcripts, missing crucial non-coding and non-polyadenylated RNAs.
This limitation hinders comprehensive analysis of cellular heterogeneity, alternative splicing, and cell cycle regulation.

Purpose of the Study:

To develop a novel method, VASA-seq, for capturing the total transcriptome in single cells.
To enable deeper insights into cellular dynamics during embryonic development.

Main Methods:

VASA-seq involves fragmenting and tailing all RNA molecules after cell lysis.
The method is adaptable to both plate-based and droplet microfluidic platforms.
Applied to over 30,000 single cells from developing mouse embryos.

Main Results:

Discovered novel cell type markers, including non-coding RNAs.
Enabled accurate in vivo cell cycle analysis using non-polyadenylated histone genes.
Improved RNA velocity analysis, accurately reconstructing blood maturation trajectories.
Provided comprehensive analysis of alternative splicing during mammalian development, revealing significant rearrangements in blood and heart development.

Conclusions:

VASA-seq significantly expands the scope of single-cell transcriptomic analysis.
The method offers unprecedented resolution for studying developmental processes, RNA regulation, and cell fate decisions.