ChIP-Seq (chromatin immunoprecipitation sequencing) combines the highly effective chromatin immunoprecipitation (ChIP) methodology with next generation sequencing (NGS) to analyze protein-DNA interactions. These interactions are crucial for numerous biological processes involved in normal development and disease progression, such as gene regulation, checkpoint regulation, DNA repair, and DNA synthesis. ChIP-Seq is a valuable tool for discerning and quantifying the specific DNA sequences where proteins bind, or epigenetic modifications exist.

ChIP-Seq Features & Benefits

Utilizes NGS technology to generate millions of reads across each sample, driving discovery

Offers higher resolution, cleaner data, and the superior ability to identify novel enrichment sites compared to ChIP-array technology

Comprehensive bioinformatics solutions

Selects any chromatin immunoprecipitated protein and modifications for analysis, including transcription factors, structural proteins, protein modifications, and DNA modifications

Low-input DNA requirement

Fast and cost-effective

What is ChIP-Seq?

ChIP-Seq is a technique used to identify genomic locations where specific proteins bind to DNA and investigate protein-DNA interactions at the genome-wide level. ChIP-Seq provides insight into the regulation of gene expression, chromatin structure, and mechanisms of epigenetic processes.


What is the difference between ATAC-Seq vs Chip-Seq?

ATAC-Seq (assay for transposase-accessible chromatin using sequencing) and Chip-Seq both use high-throughput sequencing to study chromatin features and function but differ in starting material, target molecules, and application. ATAC-Seq uses DNA as the starting material, ideally by lysing the cell to isolate nuclei, and involves the use of a hyperactive Tn5 transposase. ATAC-Seq indicates regions in the open chromatin landscape that are accessible for regulatory processes and identifies regulatory elements such as promoters and enhancers.

ChIP-Seq uses cross-linked chromatin as starting material and uses immunoprecipitation of protein-DNA complexes to analyze protein-DNA interactions. Using antibodies against the target protein to map the genomic locations where the protein is bound, ChIP-Seq generates data on protein-DNA interactions. This method provides lower resolution compared to ATAC-Seq, which provides high-resolution data at the nucleotide level regarding chromatin accessibility. Identifying where specific proteins are bound, ChIP-Seq offers insights into transcription-factor binding sites, histone modification sites, and other protein-DNA interactions.


ChIP-Seq Workflow

Extensive Quality Control is Performed at the Conclusion of Each Step of the Process
  • Building

    Experimental Design

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    Library Preparation

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    Data Analysis


ChIP-Seq Sample Submission Guidelines

GENEWIZ from Azenta accepts chromatin immunoprecipitated DNA (ChIP DNA) and plant tissue for ChIP-Seq projects. Please visit our Sample Submission Guidelines page for details.



All customers receive their raw data as FASTQ files. Peak enrichment analysis and customizable data analysis packages are available by request.


For information on our NGS platforms as well as recommended configurations of your projects, please visit the NGS Platforms page. Azenta does not guarantee data output or quality for sequencing-only projects.

10x Genomics

How To Order

Email | Phone 1-877-436-3949, Ext. 1