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Related Experiment Video

Updated: Jul 23, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Mapping alternative polyadenylation in human cells using direct RNA sequencing technology.

Mareike Polenkowski¹, Aldrige Bernardus Allister², Sebastian Burbano de Lara³

¹Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, 30623 Hannover, Germany.

|July 11, 2023

Summary

This study presents a protocol for genome-wide detection of alternative cleavage and polyadenylation (APA) using direct RNA sequencing. The method enables the identification of mRNA isoforms with varying 3' untranslated regions.

Keywords:

Gene Expression Sequence Analysis

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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:

Alternative cleavage and polyadenylation (APA) is a key biological process.
APA generates diverse messenger RNA (mRNA) isoforms.
These isoforms possess distinct 3' untranslated regions (3' UTRs).

Purpose of the Study:

To provide a detailed protocol for genome-wide APA detection.
To leverage direct RNA sequencing technology for APA analysis.
To outline the necessary computational analysis steps.

Main Methods:

RNA sample preparation
Library preparation for direct RNA sequencing
Nanopore sequencing
Computational data analysis

Main Results:

A comprehensive protocol for genome-wide APA detection is described.
The protocol integrates direct RNA sequencing with computational analysis.
It covers all steps from sample preparation to data interpretation.

Conclusions:

The presented protocol enables efficient genome-wide APA detection.
This method is valuable for studying mRNA isoform diversity.
The protocol requires expertise in molecular biology and bioinformatics.