What sample volume is required for cfChIP-seq?

Our optimized workflow works with as little as 1–4 mL of plasma or serum per sample.

Which species are supported?

Human, mouse, and rat samples are routinely supported. Other species can be evaluated on request.

What histone marks can be analyzed?

Common marks include H3K4me3, H3K27ac, and H3K36me3, but we can adapt antibody panels depending on your research goals.

How do you ensure data quality?

Strict quality control is applied at every stage, from cfDNA extraction and library construction to sequencing and bioinformatics analysis.

Can cfChIP-seq data be integrated with other omics datasets?

Yes. We provide optional multi-omics integration, such as RNA-seq or methylation data, for a more comprehensive view of gene regulation.

What formats will the results be delivered in?

Data are provided in standard formats (FASTQ, BAM, BED, and annotation tables) along with visualization-ready reports.

cfChIP-seq Liquid Biopsy | Plasma cfDNA Profiling

Introduction

Why cfChIP-seq Matters

Conventional cfDNA assays typically examine mutations, methylation, or fragmentation. While these methods provide valuable information, they often miss a key dimension of biology: the regulatory activity of genes at the time DNA is released into plasma.

cfChIP-seq addresses this gap by profiling histone modifications preserved on circulating nucleosomes. These marks serve as direct indicators of transcriptional programs, offering a dynamic view of how cells regulate gene expression.

For researchers, this enables:

Dynamic insights: Access information on recent transcriptional activity rather than static genetic alterations.
Functional context: Connect cfDNA fragments to promoters, enhancers, and regulatory elements for a clearer view of gene regulation.
Tissue and cell-type resolution: Differentiate contributions from various tissues or cell populations based on characteristic histone modification patterns.
Research versatility: Apply cfChIP-seq to diverse studies, from cancer biology to organ physiology and developmental processes.
Non-invasive accessibility: Extract chromatin-level information directly from plasma samples, without the need for solid tissue.

By transforming plasma cfDNA into a real-time epigenomic readout, cfChIP-seq opens new opportunities for understanding gene regulation and cellular states in a wide range of research fields.

Key Features of Our cfChIP-seq Service

Feature	What It Means for You
Low sample requirement	Obtain high-quality data from minimal plasma input, suitable for limited or valuable collections.
Flexible histone mark selection	Choose antibodies targeting promoters, enhancers, or elongation marks to match your research goals.
High specificity enrichment	Optimized immunoprecipitation yields clear signals with reduced background noise.
Low-input library preparation	Tailored protocols ensure reliable sequencing from scarce cfDNA.
Rigorous QC workflow	Quality control at every stage guarantees consistency and reproducibility.
Integrated technical support	Expert consultation and bioinformatics guidance throughout your project.

Workflow

Workflow Overview

Our cfChIP-seq workflow is designed to maximize data quality while keeping the process straightforward for researchers. From plasma to interpretable results, the steps include:

Plasma preparation: Guidance on sample collection, anticoagulant use, and plasma separation to preserve cfDNA integrity.
cfDNA immunoprecipitation: Enrichment of nucleosomes carrying specific histone marks using validated antibodies.
Library construction & sequencing: Optimized protocols for low-input cfDNA ensure high-quality libraries and reliable sequencing output.
Data processing & QC: Pre-processing, alignment, and rigorous quality checks confirm signal enrichment and reproducibility.
Bioinformatics interpretation: Histone mark landscapes, differential analysis, and functional enrichment provide context for your research questions.

This streamlined workflow allows researchers to explore chromatin dynamics directly from plasma cfDNA, without the need for invasive sampling.

cfChIP-seq workflow showing plasma collection, cell-free chromatin in plasma, immunoprecipitation of histone-modified nucleosomes, and genome-wide bioinformatics analysis.

Bioinformatics

Bioinformatics Analysis

cfChIP-seq bioinformatics analysis workflow with three stages: quality control, peak identification and annotation, and differential binding analysis

Raw sequencing reads are only the beginning. Our dedicated bioinformatics pipeline transforms cfChIP-seq data into meaningful biological insights.

Quality assessment – Adapter trimming, read filtering, and alignment statistics ensure reliable downstream analysis.
Peak identification – Sensitive detection of histone mark–enriched regions across the genome.
Annotation & visualization – Linking peaks to promoters, enhancers, or gene bodies, with genome browser snapshots for direct inspection.
Differential analysis – Comparative profiling between sample groups to identify changes in regulatory activity.
Motif discovery – Detection of transcription factor binding motifs associated with enriched regions.
Functional enrichment – GO and KEGG pathway analysis reveal the biological processes and signaling networks connected to observed histone modifications.
Optional integrative analysis – Combine cfChIP-seq data with RNA-seq, methylation, or other omics layers for a multidimensional view of gene regulation.

This comprehensive analysis suite supports researchers in moving from raw sequencing output to publication-ready discoveries.

Deliverables

Data Deliverables

When your cfChIP-seq project is completed, you will receive:

Raw sequencing data – FASTQ files with quality-checked reads.

Aligned data – BAM files mapped to the reference genome.

Peak call files – BED files and enrichment statistics for identified histone modification regions.

Annotation results – Peaks linked to promoters, enhancers, and associated genes.

Differential profiles – Comparative analyses between groups, with visual outputs such as heatmaps, volcano plots, PCA, and circos plots.

Motif and pathway analysis – Results from transcription factor motif discovery, GO, and KEGG enrichment.

Visualization package – Genome browser snapshots and publication-ready figures.

All deliverables are provided in standard formats widely accepted in the research community, ensuring seamless integration into your downstream analyses and publications.

Demo

Sample Requirements

Category	Guidelines
Sample type	Plasma or serum
Sample volume	1–4 mL per sample
Species	Human, mouse, and rat; other species require evaluation
Collection	Collect venous blood in EDTA anticoagulant tubes; invert gently to mix
Plasma separation	Separate plasma promptly after collection; adding protease inhibitors is recommended
Storage	Store at –20 °C or lower to preserve cfDNA integrity
Shipping	Transport on dry ice in secure, sealed containers

Applications

Applications in Research

cfChIP-seq extends the utility of liquid biopsy beyond genetic or methylation studies, opening new opportunities for epigenomic exploration across diverse fields. Researchers can apply this technology to:

Cancer biology – Characterize tumor subtypes through distinct histone modification landscapes and explore regulatory heterogeneity in circulating DNA.
Organ physiology and pathology – Detect transcriptional signatures of specific organs such as liver, heart, or kidney to study functional states and cellular stress responses.
Transplantation research – Differentiate donor- and recipient-derived nucleosome signals to investigate immune compatibility and graft biology.
Immunology – Track immune cell activity and regulatory programs reflected in plasma nucleosomes.
Developmental biology – Gain non-invasive insights into tissue contributions and gene regulation during different developmental stages.

By mapping histone modifications in circulating nucleosomes, cfChIP-seq provides a dynamic window into gene regulation that can complement mutation, methylation, or expression-based studies.

Case Study

Title: Liquid biopsy epigenomic profiling for cancer subtyping

Journal: Nature Medicine

Method: cfChIP-seq, Low-pass whole-genome sequencing, cfMeDIP-seq

Authors: Sylvan C. Baca, Ji-Heui Seo, Matthew P. Davidsohn et al.

Highlight:

Analyzed ~1 ml of plasma to generate epigenomic profiles targeting both histone modifications (e.g. H3K4me3, H3K27ac) and DNA methylation, using immunoprecipitation‐based methods.

Created over 1,200 profiles from cancer patients covering 15 cancer types, enabling classification of tumor histologic subtypes based on chromatin signals.
Identified regulatory elements whose activity in plasma correlates with ctDNA content ("CREs"), including promoters and enhancers near developmental transcription factor genes. These CREs reflect cancer‐specific transcriptional programs.
Enhancer profiling (via H3K27ac) detected epigenetic changes not captured by methylation alone, such as active promoter/enhancer signals for proto‐oncogenes and lineage‐defining transcription factors.

This work highlights how cfChIP-seq provides researchers with a powerful liquid biopsy tool to study chromatin regulation and disease-associated transcriptional landscapes.

Plasma enhancer profiling enables detection of NE-diff across multiple cancers.

Advantages

Why Choose CD Genomics

Selecting the right partner is crucial for advanced liquid biopsy research. CD Genomics combines technical expertise with a researcher-first approach to make cfChIP-seq accessible, reliable, and insightful.

Expertise in cfDNA epigenomics – Deep understanding of chromatin biology and cfDNA sequencing enables robust project design and execution.
Optimized workflows – Tailored protocols for low-input plasma samples ensure data quality without compromising sample integrity.
Comprehensive analysis – From sequencing to advanced bioinformatics, all steps are integrated to deliver complete solutions.
Customization options – Flexible antibody panels and analysis strategies can be adapted to match unique research goals.
Reliable data delivery – Standardized reporting formats and high-quality visualizations make results immediately usable.
Dedicated support – Our scientific team provides guidance at every stage, from sample preparation advice to result interpretation.

With CD Genomics, you gain more than sequencing data—you gain a partner committed to advancing your research with precision and clarity.

FAQ

Frequently Asked Questions (FAQs)

Q1. What sample volume is required for cfChIP-seq?
- - A1. Our optimized workflow works with as little as 1–4 mL of plasma or serum per sample.
Q2. Which species are supported?
- - A2. Human, mouse, and rat samples are routinely supported. Other species can be evaluated on request.
Q3. What histone marks can be analyzed?
- - A3. Common marks include H3K4me3, H3K27ac, and H3K36me3, but we can adapt antibody panels depending on your research goals.
Q4. How do you ensure data quality?
- - A4. Strict quality control is applied at every stage, from cfDNA extraction and library construction to sequencing and bioinformatics analysis.
Q5. Can cfChIP-seq data be integrated with other omics datasets?
- - A5. Yes. We provide optional multi-omics integration, such as RNA-seq or methylation data, for a more comprehensive view of gene regulation.
Q6. What formats will the results be delivered in?
- - A6. Data are provided in standard formats (FASTQ, BAM, BED, and annotation tables) along with visualization-ready reports.

Get Started

Get Started with cfChIP-seq

Advance your research with a liquid biopsy solution that captures gene regulation directly from plasma cfDNA. CD Genomics provides optimized workflows, high-quality sequencing, and comprehensive analysis tailored to your study goals.

Whether you are exploring chromatin dynamics, characterizing tissue-of-origin signals, or integrating epigenomic data into broader studies, our cfChIP-seq service delivers results you can trust.

Contact us today to discuss your cfChIP-seq project or request a custom quote.

Looking for additional approaches? Explore our full range of Liquid Biopsy Solutions to discover complementary services for your research.

CD Genomics cfDNA detection technologies including methylation, hydroxymethylation, histone modifications, WGS, and WES.

cfChIP-seq for Liquid Biopsy Research