Comprehensive exploration of the methylome

NGS enhances epigenetic studies with high coverage density and flexibility

Methylation Sequencing

Cytosine methylation can significantly modify temporal and spatial gene expression and chromatin remodeling. Leveraging the power of next-generation sequencing (NGS), both genome-wide analysis and targeted approaches can provide researchers with insight into methylation patterns at a single nucleotide level.

Advantages of methylation sequencing:

  • Discover methylation patterns of CpG, CHH, and CHG regions across the human genome
  • View methylation at practically every cytosine in the genome across most species with a genome-wide approach known as whole-genome bisulfite sequencing (WGBS) 
  • Capture full sample diversity with small amounts of DNA
  • Cover emerging regions of interest in the human genome identified by ENCODE, FANTOM5, and the Epigenomics RoadMap Consortium with targeted methylation sequencing
Advancing DNA Methylation Studies with NGS

This eBook discusses genomics applications in gene expression and regulation research. See how workflows can impact study results.

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Many approaches leverage the high quality and sensitivity of NGS for methylation analysis. Most methods rely on bisulfite conversion of DNA to detect unmethylated cytosines. Bisulfite conversion changes unmethylated cytosines to uracil during library preparation. Converted bases are identified (after PCR) as thymine in the sequencing data, and read counts are used to determine the % methylated cytosines.

Bisulfite conversion sequencing can be done with targeted methods such as amplicon methyl-seq or target enrichment, or with whole-genome bisulfite sequencing. Additionally, alternative chemistries like OxBS and TAB-Seq can be used with NGS for identification of hydroxymethylation (5-hMc) in conjunction with methylation (5-mc) analysis.

See the Field Guide to DNA Methylation Analysis for a deep dive into methylation analysis methods.

Perturbation of Methylation

More than 90% of the world’s sequencing data is generated using Illumina NGS technology.*

Illumina offers a fully supported workflow, from library preparation to data analysis, for methylation sequencing.

Click on the below to view products for each workflow step.

Create target enrichment-based bisulfite sequencing libraries from as little as 500 ng of human DNA samples.

NextSeq 550 System

Flexible benchtop sequencer supporting multiple applications, sequencing 1 DNA sample per 2 flow cells.

HiSeq 4000 System

High throughput and low cost to sequence 2-3 samples per flow cell.

NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.

MethylSeq App

For WGBS or targeted methylation sequencing. Maps bisulfite-treated sequencing reads to the genome of interest and performs methylation calls using the Bismark algorithm.

MethylKit App

MethylKit analyzes sequencing data from reduced-representation bisulfite sequencing (RRBS) as well as whole-genome bisulfite sequencing.

BaseSpace Data Repository

View example WGBS data generated using Illumina library preparation kits and sequencing instruments (use the “Methyl-Seq” category filter).

Methods Guide

Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.

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Methods Guide
Epigenetics and Cancer
Epigenetic Changes in Cancer

Studies of epigenetic alterations in cancer, such as aberrant methylation and altered transcription factor binding, can provide insight into important tumorigenic pathways. Learn more about analyzing epigenetic changes in cancer.

Complex Disease Genomics
Methylation Profiling for Complex Disease

Genome-wide methylation sequencing can help researchers understand the functional mechanisms at work in complex neurological, immunological, and other diseases. Learn more about complex disease research.

The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells.

J Biotechnol 199 38-46 2015

View Summary

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.

Cell Rep 10 1386-97 2015

View Summary

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors.

Nat Biotechnol 33 769-74 2015

View Summary
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Peter Laird: Epigenetics, DNA Methylation, and Arrays
Peter Laird: Epigenetics, DNA Methylation, and Arrays

Peter Laird, PhD, discusses his studies of epigenetics and the role DNA methylation may play in contributing to cancer.

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Whole-Genome Bisulfite Sequencing Library Prep
Whole-Genome Bisulfite Sequencing Library Prep

Efficient nanogram-scale library preparation, sequencing, and analysis of DNA methylation.

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Epigenetic Contributions to Addiction
Epigenetic Contributions to Addiction

Marilee Morgan discusses the use of NGS to correlate epigenetic signatures with brain image scans of substance abusers.

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Methylation and Metastasis
Methylation and Metastasis

Researchers investigate the epigenetics behind cancer metastasis using DNA methylation microarrays and NGS.

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Library Prep for WGBS with Fraz Syed
Library Prep for WGBS with Fraz Syed

Illumina scientist Fraz Syed explains library preparation for whole-genome bisulfite sequencing.

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Library Prep for WGBS with Fraz Syed
MethylSeq App for DNA Methylation Calling

Learn more about this bioinformatics solution for analyzing NGS methylation data.

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*Data calculations on file. Illumina, Inc., 2015