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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: Feb 20, 2026

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

3' End Sequencing Library Preparation with A-seq2.

Georges Martin¹, Ralf Schmidt¹, Andreas J Gruber¹

¹Computational and Systems Biology, Biozentrum, University of Basel.

Journal of Visualized Experiments : Jove

|October 21, 2017

Summary

This summary is machine-generated.

The A-seq2 protocol efficiently maps messenger RNA (mRNA) polyadenylation sites genome-wide. This method aids in studying pre-mRNA 3' end processing regulation in various cell types.

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Last Updated: Feb 20, 2026

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

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

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Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices

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Published on: March 26, 2018

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Pre-mRNA cleavage and polyadenylation reactions are complex and dynamic.
Cellular differentiation influences messenger RNA (mRNA) 3' untranslated region (UTR) lengths, with differentiated cells producing long 3' UTRs and proliferating cells producing short 3' UTRs.

Purpose of the Study:

To describe the A-seq2 protocol for genome-wide mapping of polyadenylation sites.
To enable the study of pre-mRNA 3' end processing regulation.

Main Methods:

The A-seq2 protocol enriches for fully processed mRNAs using their poly(A) tails.
A DNA adaptor with deoxyuracil facilitates precise processing of mRNA 3' end fragments for sequencing.
The protocol requires approximately 8 hours of hands-on time, excluding cell culture and overnight ligations.

Main Results:

A-seq2 provides an efficient and reliable method for mapping pre-mRNA 3' ends.
Associated software facilitates the analysis of sequencing data.
The protocol is effective even with limited cell numbers (10^6 or fewer).

Conclusions:

A-seq2 is a valuable tool for investigating polyadenylation site dynamics and regulation.
The protocol and analysis software offer a comprehensive solution for pre-mRNA 3' end mapping across diverse experimental conditions.