Precise analysis of DNA–protein binding sequences

Combining chromatin immunoprecipitation with NGS for genome-wide surveys of gene regulation

Chromatin Immunoprecipitation Sequencing (ChIP-Seq)

By combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP sequencing (ChIP-Seq) is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. Following ChIP protocols, DNA-bound protein is immunoprecipitated using a specific antibody. The bound DNA is then coprecipitated, purified, and sequenced.

The application of next-generation sequencing (NGS) to ChIP has revealed insights into gene regulation events that play a role in various diseases and biological pathways, such as development and cancer progression. ChIP-Seq enables thorough examination of the interactions between proteins and nucleic acids on a genome-wide scale.

ChIP-Seq in 3 Simple Steps

Perform genome-wide surveys of gene regulation with this seamless workflow solution.

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Unlike arrays and other approaches used to investigate the epigenome, which are inherently biased because they require probes derived from known sequences, ChIP-Seq does not require prior knowledge. ChIP-Seq delivers genome-wide profiling with massively parallel sequencing, generating millions of counts across multiple samples for cost-effective, precise, unbiased investigation of epigenetic patterns. Additional advantages include:

  • Captures DNA targets for transcription factors or histone modifications across the entire genome of any organism
  • Defines transcription factor binding sites
  • Reveals gene regulatory networks in combination with RNA sequencing and methylation analysis
  • Offers compatibility with various input DNA samples
Advantages of ChIP-Seq

ChIP-Seq identifies the binding sites of DNA-associated proteins and can be used to map global binding sites for a given protein. ChIP-Seq typically starts with crosslinking of DNA-protein complexes. Samples are then fragmented and treated with an exonuclease to trim unbound oligonucleotides. Protein-specific antibodies are used to immunoprecipitate the DNA-protein complex. The DNA is extracted and sequenced, giving high-resolution sequences of the protein-binding sites.

ChIP-Seq Process
NGS Proves Invaluable for Biomarker Discovery
Breast cancer

Researchers use ChIP-Seq, RNA-Seq, and exome sequencing to study gene expression profiles associated with cancer and uncover biomarkers.

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Exploring the Unknown: NGS Supports Species Research
Marine species research

OIST researchers use Illumina NGS to sequence various ocean and land species. The institute offers a variety of services, such as de novo sequencing, ChIP-Seq, and RNA-Seq. 

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Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.* Illumina offers integrated workflows that simplify sequencing, from library preparation to data analysis. 

ChIP-Seq may require only a few reads (~5-15 million) for a highly targeted transcription factor, and many more reads (~50 million) for a ubiquitous protein such as a histone mark pull-down.

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

TruSeq ChIP Library Prep Kit
Simple, cost-effective method for preparing ChIP-Seq libraries from ChIP-derived DNA.
MiSeq System

Focused power to sequence 1–6 ChIP-Seq samples per run.

NextSeq 1000 & 2000 Systems

Groundbreaking benchtop sequencers allow you to explore new discoveries across a variety of current and emerging applications, with higher efficiency and fewer restraints.

NovaSeq 6000 System

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

Illumina sequencing platform

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.

BaseSpace ChIP-Seq App

Identifies transcription factor binding sites using MACS2 and discovers motifs within the peaks using HOMER.

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

BaseSpace Correlation Engine

A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.

Optimal Cluster Density Best Practices

Watch Illumina scientists discuss how over- and underclustering can affect your sequencing data. Learn about common clustering issues and ways to prevent them.

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How to Achieve Consistent Cluster Density

Cluster density has a significant impact on run performance, specifically data quality and total output. Learn how to achieve more consistent cluster densities.

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Cancer Epigenetics
Cancer Epigenetics

Studies of epigenetic changes in cancer, such as aberrant methylation and altered transcription factor binding, can offer insights into important tumorigenic pathways. Learn more about cancer epigenetics.

Gene Expression Analysis
Gene Expression Analysis

Gene expression studies can provide visibility into how genomic and environmental changes contribute to various diseases. Learn how to profile gene expression.

Chromatin Accessibility Analysis

ATAC-Seq is a popular method for determining chromatin accessibility across the genome. Subsequent experiments often include ChIP-Seq, Methyl-Seq, or Hi-C-Seq. Learn more about ATAC-Seq.

Methylation Sequencing
Methylation Sequencing

NGS-based methylation sequencing approaches offer numerous benefits, including the ability to profile methylation patterns at a single nucleotide level. Learn more about methylation sequencing.

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. 

Researchers used Illumina sequencing to perform genome-wide chromatin immunoprecipitation and RNA expression profiling during B-cell lymphomagenesis.

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RNA-Seq analysis and whole genome DNA-binding profile of the Vibrio cholerae histone-like nucleoid structuring protein (H-NS).

The authors used Illumina sequencing for differential RNA-seq and chromatin immunoprecipitation sequencing using an anti-FLAG M2 monoclonal antibody.

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ChIP-Seq and Microarray Reveal a Sox9-Controlled Cancer-Specific Gene Network

Transcriptional profiling and in vivo ChIP-Seq studies uncover a cancer-specific gene network regulated by Sox9 that links tumor initiation and invasion. 

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Nature Epigenome Roadmap
Nature Epigenome Roadmap

The NIH Epigenome Roadmap highlights research characterizing epigenomic landscapes in primary human tissues and cells.

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Blueprint Epigenome Project
Blueprint Epigenome Project

Blueprint is a European research project that applies functional genomic analysis to understand the human epigenome.

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ChIP-Seq Data Analysis
ChIP-Seq Data Analysis

An overview of ChIP-Seq data processing using BaseSpace Correlation Engine.

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ChIP-Seq Profiling of ERα Binding Sites
ChIP-Seq Profiling of ERα Binding Sites

Researchers from Radboud University describe a ChIP-Seq method for analyzing estrogen receptor alpha binding sites.

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