Introduction to Chromatin Immunoprecipitation Sequencing (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.
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&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||≥ 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 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||
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.
SET Domain–Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence
Cancer ResearchIssue Date: 2019IF: 9.727DOI: 10.1158/0008-5472
Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes
Nucleic acids researchIssue Date: 15 July 2019IF: 11.501DOI: 10.1093/nar/gkz594
Hematopoietic PBX-interacting protein mediates cartilage degeneration during the pathogenesis of osteoarthritis
Nature communicationsIssue Date: 18 January 2019IF: 12.121DOI: 10.1038/s41467-018-08277-5
E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the EGFR and c-MET Oncogenes by Destabilizing the Histone Demethylase KDM5C
Cancer ResearchIssue Date: 2018IF: 9.727DOI: 10.1158/0008-5472
Targeting Epigenetic Crosstalk as a Therapeutic Strategy for EZH2-Aberrant Solid Tumors
cellIssue Date: 20 September 2018IF: 38.637DOI: 10.1016/j.cell.2018.08.058
Distribution of MAPQ
Plot of Strand Cross Correlation
Distance Distribution of Peaks to TSS
Peak Distribution in Functional Gene Regions
Diagram of GO Enrichment
KEGG Enrichment Scatter Plot