ChIP Sequencing

Overview Features Workflow & Data Analysis Requirements Demo Cases & FAQ Resources Inquiry

ChIP-Seq, short for Chromatin immunoprecipitation sequencing, is a next-generation based sequencing method to comprehensively study the interaction between proteins and DNA. It takes advantage of the specificity of the antigenic antibody response to provide a fidelity reflection of the binding of protein factors to genomic DNA in vivo.


In recent years, due to the continuous development and refinement of ChIP-Seq its application has evolved from the study of interactions between target proteins and known target sequences to the study of interactions between target proteins and unknown sequences throughout the genome; from studying the interaction of a target protein with DNA to the interaction of two proteins co-associated with DNA; from studying the modification of histones in promoter regions to protein complexes bound to DNA sequences. And ChIP-Seq can be widely used in transcription factor binding sites (TFBSs) and histone modification studies. This technique uses reagents such as formaldehyde to cross-link and immobilize protein-DNA complexes in cells, lyses and ultrasonic processing cells, and immunoprecipitates them with antibodies specific to the target protein (or labeled antibodies) to obtain the target protein-DNA complexes. High-throughput sequencing of the DNA in the cross-linked isolated complexes allows the identification of DNA sequences that may interact with the target protein.

Genome-wide mapping of protein-DNA interactions and epigenetic marks is essential for a comprehensive understanding of transcriptional regulation in organisms. DNA-binding proteins, including transcription factors, epigenetic factors, and chromatin modifiers, control gene expression in the organism. Localizing the binding sites of DNA-binding proteins in the genome is essential for decoding gene regulatory networks.

By performing RNA-Seq after overexpression/knockout/disruption of a specific gene to search for significantly up- or down-regulated downstream genes affected by the gene; ChIP-Seq can search for genetic information of DNA binding sites where histones, transcription factors, etc. interact. When RNA differentially expressed genes are analyzed in conjunction with ChIP-Seq technology, it helps us to explore the mechanisms by which transcription factors, cofactors and histone modifications regulate gene expression.


High ThroughputGenome-WideBioinformatics AnalysisOne-stop Service
Cost-effective transcriptional profiling solution for large sample-size assays.Profile all open chromatins, known and novel.Our integrated bioinformatics pipeline can be tailored to suit your project.Provides one-stop service for library construction, sequencing, sample QC and data analysis.

Project Workflow

Sample Preparation

1. Sample Preparation

RNA purification;
quality assessment and quantification.

Library Preparation

2. Library Preparation

RNA fragmentation;
cDNA library preparation.


3. Sequencing

Illumina HiSeq;
PE 50/75/100/150.

Data Analysis

4. Data Analysis

Visualize and preprocess results, and perform custom bioinformatics analysis.

ChIP Sequencing

Bioinformatics Analysis Pipeline

In-depth data analysis:

  • Data quality control;
  • Peak calling and annotation;
  • Fragment size distribution;
  • Gene ontologies;
  • KEGG pathways;
  • Differential analysis.

Sample Requirements

Cell sample ≥ 50,000 cells; Nucleus sample ≥ 50,000 nuclei

Sample storage: Nuclei can be frozen at –20˚C for up to two days, avoid repeated freezing and thawing.

Shipping Method: Samples are supposed to stored in a 1.5 mL microcentrifuge tube, sealed with sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, full statistical analysis & alignments, custom analysis reports on customer request.

Demo Results

Distribution of reads mapped to the genomeDistribution of reads mapped to the genome

Distribution of peaksDistribution of peaks

Motif analysisMotif analysis

GO enrichmentGO enrichment

KEGG pathway enrichmentKEGG pathway enrichment

KEGG pathway enrichmentKEGG pathway enrichment

Case Studies



  1. Massie CE, Mills IG. Mapping protein–DNA interactions using ChIP-sequencing. Transcriptional Regulation: Springer; 2012. p. 157-73.
  2. Furey TS. ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nature Reviews Genetics. 2012;13(12):840-52.
  3. Schmidt D, Wilson MD, Spyrou C, et al. ChIP-seq: using high-throughput sequencing to discover protein–DNA interactions. Methods. 2009;48(3):240-8.
  4. Fullwood MJ, Ruan Y. ChIP‐based methods for the identification of long‐range chromatin interactions. Journal of cellular biochemistry. 2009;107(1):30-9.
* For Research Use Only. Not for use in diagnostic procedures.

Research Areas
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