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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 16, 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

Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.

Oguzhan Begik¹, Leszek P Pryszcz¹, Adnan Muhammad Niazi²

¹Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

Nature Protocols

|July 8, 2025

Summary

This summary is machine-generated.

This study introduces Nanopore 3' end-capture sequencing (Nano3P-seq) for analyzing RNA poly(A) tail dynamics. The method accurately quantifies RNA abundance, tail length, and composition for diverse RNA types.

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Last Updated: Sep 16, 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

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

RNA polyadenylation is vital for RNA processing, affecting stability, translation, and decay.
Poly(A) tail length is a key determinant of mRNA function and regulation.
Current methods for analyzing poly(A) tails can be limited in scope or resolution.

Purpose of the Study:

To present a detailed protocol for Nanopore 3' end-capture sequencing (Nano3P-seq).
To introduce PolyTailor software for analyzing poly(A) tail length and composition.
To enable single-molecule resolution analysis of RNA tail dynamics across various RNA types.

Main Methods:

Development and validation of the Nano3P-seq protocol using Nanopore sequencing.
Utilizing a template switching-based approach for cDNA sequencing from the 3' end.
Employing the PolyTailor software for data analysis and prediction of tail characteristics.

Main Results:

Nano3P-seq accurately estimates transcript abundances, poly(A) tail lengths, and composition.
The method successfully analyzes coding and noncoding RNAs, including mRNAs, snoRNAs, and rRNAs.
The protocol is compatible with R10.4 flow cells and can be completed within a day.

Conclusions:

Nano3P-seq offers a comprehensive and reproducible method for studying RNA tail dynamics.
The protocol is adaptable to various RNA sample preparation methods.
This technique enhances the study of transcriptome-wide tail heterogeneity.