ChIP-Seq Service

ChIP-seq technology is generated by combining chromatin immunoprecipitation (ChIP) with next-generation sequencing (NGS) technology, which can efficiently detect DNA segments interacting with histones, transcription factors, etc. on a genome-wide scale. The target protein-binding DNA fragments are first specifically enriched by ChIP, and then purified and library constructed. The enriched DNA fragments are then subjected to high-throughput sequencing. Millions of sequences will be obtained and corresponded to the genome to obtain genome-wide information on the level of histone modifications and transcription factor binding sites. The application of NGS to ChIP has revealed several clues to gene regulatory events that play a role in various diseases and biological pathways, such as development and cancer development.

ChIP-seq is a core method for epigenomic studies that detects protein/DNA binding and histone modification sites throughout the genome. Genome-wide analysis of histone modifications, such as enhancer analysis and genome-wide chromatin state annotation, allows systematic analysis of how the epigenome contributes to cell identity, development, genealogical specification and disease. Advances in sequencing technology have allowed us to compare hundreds of samples simultaneously. Such large-scale analyses have the potential to reveal high-dimensional levels of interrelationship and annotate new functional genomic regions from scratch.

ChIP-Seq can be used to localize the overall binding site of a given protein. Microarrays and other methods for studying epigenomes are often inherently biased because they require probes from known sequences. chIP-Seq does not require any a priori knowledge. ChIP-Seq provides genome-wide mapping through massively parallel sequencing, generating multi-million count analysis covering multiple samples for economical and accurate analysis.

Creative Proteomics offers a one-stop shop for Chip-seq services, all of which can be performed by a dedicated NGS experimental and data analysis team. In addition, we also offer ChIP services.

ChIP-seq analysis workflowChIP-seq analysis workflow (Nakato et al., 2017)

(A) Sample preparation, sequencing and mapping. This process is common to (B) and (C).
(B) Small-scale analysis (single or several samples). In this case, peak calling strategies and parameters can be adjusted for the properties of each sample.
(C) Large-scale analysis (many samples). The rectangles on the left indicate different experiments (e.g., the same analysis for different cell types). Since the combined analysis is sensitive to the quality of the input samples and difficult to adjust on a sample-by-sample basis, automatic filtering of low-quality data for objective quality metrics for multilateral quantitative assessment is required.

Advantages of ChIP-seq Services

Capture transcription factors or histone modified DNA targets throughout the genome of any organism

Identify binding sites for transcription factors

Combines RNA sequencing and methylation analysis to reveal gene regulatory networks

Compatible with DNA samples of varying starting volumes

ChIP-seq Data Analysis

1) Downstream data pre-processing and filtering

2) Matching to the reference genome

3) Identification of DNA bound to the target protein and its binding region

4) Analysis of protein binding peaks for individual samples, including annotation of genes associated with binding peaks, GO analysis KEGG pathway enrichment analysis and motif analysis

5) Differential binding peak analysis for multiple samples, including annotation of genes associated with differential binding peaks, GO analysis, KEGG pathway enrichment analysis and motif analysis

(6) If the data can be combined with RNA-seq or lncRNA-seq data, further in-depth analysis of the regulatory mechanism of the target protein can be done.

ChIRP-seq analysis reveals genome-wide binding sites for Tug1, including a TBE upstream of the Ppargc1a promoterChIRP-seq analysis reveals genome-wide binding sites for Tug1, including a TBE upstream of the Ppargc1a promoter (Long et al., 2016).

Sample Requirements

  • Sample type: DNA samples
  • Total amount: ≥ 10 ng (human samples can be as low as 5 ng)
  • Concentration: ≥ 1 ng/μL
  • Purity: OD260/280= 1.8 - 2.0
  • DNA fragment size: distributed in the range of 100~500 bp and with distinct primary bands.

If you would like to learn more about ChIP-seq services or have other needs, please contact us. We look forward to cooperating with you.


  1. Nakato, R., & Shirahige, K. (2017). Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation. Briefings in bioinformatics, 18(2), 279-290.
  2. Long, J., Badal, S. S., et al. (2016). Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy. The Journal of clinical investigation, 126(11), 4205-4218.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.