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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 5, 2025

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling.

Ksenia Skvortsova^1,2, Ozren Bogdanovic^3,4

¹Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia. k.skvortsova@garvan.org.au.

Methods in Molecular Biology (Clifton, N.J.)

|May 19, 2021

Summary

This summary is machine-generated.

This study details computational methods for analyzing 5-hydroxymethylcytosine (5hmC) DNA modifications using TET-assisted bisulfite sequencing (TAB-seq) and APOBEC-coupled epigenetic sequencing (ACE-seq) data. These protocols enable precise 5hmC calling and statistical analysis for genome-wide profiling.

Keywords:

ACE-seq DNA hydroxymethylation DNA methylation and hydroxymethylation data analysis TAB-seq

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Last Updated: Nov 5, 2025

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Area of Science:

Epigenetics and Genomics
Molecular Biology
Bioinformatics

Background:

5-Methylcytosine (5mC) is a crucial DNA modification regulating vertebrate genome functions like gene silencing and cell fate.
TET enzymes convert 5mC to 5-hydroxymethylcytosine (5hmC), adding complexity to epigenetic regulation.
Genome-wide 5hmC profiling techniques have advanced understanding of its distribution and function.

Purpose of the Study:

To provide a detailed computational protocol for analyzing TAB-seq and ACE-seq data.
To enable accurate genomic alignment, 5hmC calling, and statistical analysis of sequencing data.
To facilitate research into the role of 5hmC in genome regulation.

Main Methods:

Genomic alignment of TAB-seq and ACE-seq sequencing reads.
5hmC calling algorithms for precise identification of modified sites.
Statistical analysis frameworks for interpreting 5hmC profiling data.

Main Results:

A robust computational pipeline for processing and analyzing TAB-seq and ACE-seq data.
Validated methods for accurate genome-wide 5hmC site identification.
Tools for statistical assessment of 5hmC distribution and significance.

Conclusions:

The presented computational protocol streamlines the analysis of 5hmC sequencing data.
Accurate 5hmC profiling is essential for understanding its role in vertebrate epigenetics.
This work supports further investigation into DNA methylation dynamics and genome regulation.