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Chromatin Immunoprecipitation Sequencing (ChIP-Seq)

Introduction to ChIP-seq

Chromatin Immunoprecipitation Sequencing (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 immuno-precipitation (ChIP) to recover specific protein-DNA complexes, with the power of next-generation sequencing (NGS) to achieve high-throughput sequencing of the recovered DNA.

As protein-DNA complexes are recovered from living cells, binding sites can be compared in different cell types and tissues, or under different conditions. At Novogene, we offer high-quality sequencing and comprehensive bioinformatics solutions for your ChIP-seq projects.

How does ChIP-seq apply?

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&Tag, etc..

Benefits of Novogene ChIP-seq

  • The output data is stable and reliable, with the guaranteed data quality of the sequencing score Q30≥ 80%.
  • 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 ≥ 50 ng (Concentration ≥ 2ng/μL) 100 bp~500bp OD260/280=1.8-2.0

Note: Sample amounts are listed for reference only. Download the Service Specifications or Sample Requirements 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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