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.
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:
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.
Researchers use ChIP-Seq, RNA-Seq, and exome sequencing to study gene expression profiles associated with cancer and uncover biomarkers.Read Interview
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.Read Interview
Simple, cost-effective method for preparing sequencing libraries from ChIP-derived DNA.
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.
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.
Focused power to sequence 1–6 ChIP-Seq samples per run.NextSeq 550 System
Flexible power to sequence 8–24 ChIP-Seq samples in parallel.NovaSeq 6000 System
Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.HiSeq 4000 System
Production power to sequence 4–150 ChIP-Seq samples in
parallel, depending on the target protein of interest.
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.
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.
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 studies can provide visibility into how genomic and environmental changes contribute to various diseases. Learn how to profile gene expression.
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.
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.
Researchers used Illumina sequencing to perform genome-wide chromatin immunoprecipitation and RNA expression profiling during B-cell lymphomagenesis.Read Publication
The authors used Illumina sequencing for differential RNA-seq and chromatin immunoprecipitation sequencing using an anti-FLAG M2 monoclonal antibody.Read Publication
Transcriptional profiling and in vivo ChIP-Seq studies uncover a cancer-specific gene network regulated by Sox9 that links tumor initiation and invasion.Read Publication
*Data calculations on file. Illumina, Inc., 2015