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Chromatin Immunoprecipitation Sequencing (ChIP-seq)

Introduction to Chromatin Immunoprecipitation Sequencing (ChIP-seq)

ChIP sequencing, or ChIP-seq provides genome-wide profiling of DNA targets for histone modification, transcription factors, and other DNA-associated proteins. It combines the selectivity of chromatin immune-precipitation (ChIP) to recover specific protein-DNA complexes, with the power of Next Generation Sequencing (NGS) to achieve high-throughput sequencing of the captured DNA fragments.

At Novogene, we offer high-quality sequencing and comprehensive bioinformatics solutions for your ChIP-seq projects. With the power of illumina NovaSeq platfrom and our project experience, we support your research on DNA-protein interactions, histone modification, transcription factors, and other epigenetic regulation.

Applications of Chromatin Immunoprecipitation Sequencing (ChIP-seq)

ChIP-seq provides regulatory solutions and meets customized research needs, such as:

  • Understanding how transcription factors regulate genes by profiling a genome-wide binding site and analyzing motif
  • Outlining histone modification patterns associated with experimental treatment or sample conditions
  • Investigating the relationships between epigenetic profiles and transcriptional regulations through joint analysis
  • Accommodating to multiple immunoprecipitated DNAs using various methods, including ChIP, Cut&Run, Cut&Tag, etc..

Benefits of Novogene’s ChIP-seq service

  • The output data is stable and reliable, with the guaranteed data quality of the sequencing score Q30≥ 85%.
  • Expert bioinformatics analysis utilizes industry-standard MACS2 software and programs with the latest version to get motif prediction, peak annotation, functional analysis, and data visualization.
  • Associated analysis is provided to explore correlations between ChIP-seq and gene expression.

ChIP-seq Specifications: DNA Sample Requirements

Sample Type Required Amount Fragment size Purity
Enriched DNA Sample ≥ 20 ng (Concentration ≥ 2 ng/μL) 100 bp~500 bp A260/280=1.8-2.0

Note: Sample amounts are listed for reference only. Download the Service Specifications to learn more. For detailed information, please contact us with your customized requests.

ChIP-seq Specifications: Sequencing & Analysis

Platform Illumina NovaSeq 6000
Read Length Pair-end 150 bp
Sequencing Depth ≥ 20 million read pairs per sample for the species with reference genome
Standard Data Analysis
  • Data Quality Control
  • Mapping onto reference genome
  • Peak calling
  • Motif prediction
  • Peak annotation and functional analysis of peak-associated genes
  • Summary of differential peaks and functional analysis of differential peak related genes
  • Visualization of ChIP-seq data

Note: Sequencing parameters and analysis contents displayed are only for reference. Download the Service Specifications to learn more. For detailed information, please contact us with your customized requests.

Project Workflow of Novogene ChIP-seq Service

Novogene ChIP-seq service comprises four steps, including sample preparation, DNA library preparation, Illumina PE150 sequencing and data analysis using bioinformatics pipelines. From DNA sampling to obtaining data reports, each step may affect the quality and quantity of data output, directly affecting the results of subsequent bioinformatics analysis. Novogene strictly checks every step, including sample quality control, library quality control, and sequencing data quality control, to ensure the high quality, accuracy and reliability of sequencing data and provide comprehensive bioinformatics analysis.

Featured Publications using Novogene ChIP-seq Service

ChIP-seq provides genome-wide profiling of DNA targets for histone modification, transcription factors, and other DNA-associated proteins. Novogene provides high-quality sequencing and comprehensive bioinformatics analysis, including peak calling, motif analysis, peak annotation, differential analysis, and related functional analysis. We summarize a publication list with Novogene ChIP-seq service.

Distribution of MAPQ

Novogene ChIP-seq Distribution of MAPQ

Plot of Strand Cross Correlation

Novogene ChIP-seq Plot of Strand Cross Correlation

Distance Distribution of Peaks to TSS

Novogene ChIP-seq Distance Distribution of Peaks to TSS

Motif Analysis

Novogene ChIP-seq Motif Analysis

Peak Distribution in Functional Gene Regions

Novogene ChIP-seq Peak Distribution in Functional Gene Regions

Diagram of GO Enrichment

Novogene ChIP-seq Diagram of GO Enrichment

KEGG Enrichment Scatter Plot

Novogene ChIP-seq KEGG Enrichment Scatter Plot

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