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.
View Recommended Workflow

  • 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. 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 analysis.

Unbiased Investigation of Epigenetic Patterns

Recommended Workflow for ChIP-Seq

1 2 3
1 Library Prep

Prepare
Your Library with

TruSeq ChIP Library Prep Kit

Simple, cost-effective method for preparing ChIP-Seq libraries from ChIP-derived DNA.

2 Sequence Efficently

Sequence
Efficiently with

HiSeq 3000/HiSeq 4000

Production power to sequence 4–150 ChIP-Seq samples in parallel, depending on the target protein of interest.

3 Analyze and Store Data

Analyze and
Store Data with BaseSpace Apps

ChIPSeq

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

Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*

In addition to industry-leading data quality, Illumina offers integrated workflows that simplify sequencing, from library preparation to data analysis.

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 Series

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

NextSeq Series

Flexible power to sequence 8–24 ChIP-Seq samples in parallel.

HiSeq Series
Production power to sequence 4–150 ChIP-Seq samples in
parallel, depending on the target protein of interest.
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.

Note: 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.

ChIP-Seq App

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

Genomatix Pathway System (GePS)

Generation and visualization of pathways, networks, and processes.

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.

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

Analyzing gene expression and regulation provides visibility into how genomic and environmental changes contribute to common disease. Learn more about gene expression profiling and regulation studies.

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

Nature 511 488-922014

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

Genom Data 5 147-1502015

View Summary
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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.

Learn More
Blueprint Epigenome Project
Blueprint Epigenome Project

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

Learn More
ChIP-Seq Data Analysis
ChIP-Seq Data Analysis

This technical note describes a simple approach to analyzing ChIP-Seq data sets.

Access PDF
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.

Access PDF

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