cfChIP-seq: cfDNA/Plasma-Nucleosome ChIP-seq Sequencing Service
Unlock insights into chromatin dynamics with our cutting-edge cfChIP-seq technology. Ideal for cancer research, immunology, and organ-specific studies. Non-invasive, low-volume plasma sampling gives you access to detailed epigenetic profiles without tissue biopsies.
Key Points:
Precise Epigenetic Insights: Study histone modifications from circulating free DNA (cfDNA) in plasma.
Non-Invasive Approach: Only 1–2 mL of plasma required for comprehensive chromatin profiling.
Optimized for Research: Perfect for cancer, immune response, and organ research.
In molecular research, decoding gene regulation and transcriptional activity is fundamental—but traditional tissue biopsies bring challenges: invasiveness, ethical hurdles, and struggles to get representative samples. That's where cfChIP-seq steps in: a non-invasive, high-resolution epigenetic profiling tool that delivers powerful insights without tissue extraction.
Unlock Epigenetic Insights from Plasma
cfChIP-seq analyzes histone modifications from circulating free DNA (cfDNA) in plasma, offering a real-time window into cellular transcriptional and epigenetic states. It captures dynamic changes in health, disease, or treatment responses—all from a simple blood sample.
What Sets cfChIP-seq Apart?
Non-Invasive, Low-Volume Sampling: Just 1–2 mL of plasma yields data that once required invasive biopsies. No more relying on hard-to-obtain tissue samples.
Targeted Histone Modification Profiling: Specific antibodies (e.g., H3K4me3 for active transcription, H3K27ac for enhancer activity, pan-H3ac for chromatin remodeling) enable precise, nucleosome-level analysis of chromatin modifications. You get exactly the epigenetic data your study needs.
Comprehensive Epigenetic Data: By capturing these marks from cfDNA, cfChIP-seq reveals transcriptional activity, gene regulation, and even tumor progression. It's a direct link to the molecular processes driving your research.
Ideal for Diverse Research
cfChIP-seq works for oncology, immunology, organ-specific studies, and beyond. Whether you're exploring cancer epigenomics, immune responses, or organ-specific diseases, it delivers rich, actionable data—no invasive procedures required. You can focus on understanding how your targets are regulated, not on sample collection hurdles.
Spotlight on Technical Excellence
cfChIP-seq leverages cutting-edge technology to deliver precise, reliable, and comprehensive epigenetic insights—here's how our service stands out in epigenetic research:
1. Antibody Specificity & Modular Options
cfChIP-seq relies on highly specific antibodies to target histone modifications, with a modular selection of options tailored to your research needs—including H3K4me3 (active transcription), H3K27ac (enhancer activity), Pan-H3ac (chromatin remodeling), and custom modifications. This flexibility ensures you get the precise epigenetic data your study requires, without unnecessary complexity.
2. Low-Input cfDNA Library Prep
Our optimized protocol handles as little as 10 ng of cfDNA—ideal for limited or precious samples. Using just 1–2 mL of plasma, we generate high-quality sequencing libraries while preserving data integrity, maximizing sensitivity even from challenging inputs.
3. Robust Analysis Pipelines
Our bioinformatics workflow is designed for reliability:
Cleanup & Alignment: We trim adapters and perform quality control to ensure high-quality reads, then map them to the reference genome to identify histone modification locations.
Peak Calling: We detect enriched genomic regions (e.g., enhancers, promoters) where specific histone marks occur—key for understanding regulatory activity.
Functional Insights: We run GO/KEGG pathway analysis (to link peaks to biological processes), motif analysis (to explore transcription factor networks), and differential peak analysis (to compare groups and uncover meaningful differences).
4. Data Interpretation & Visualization
We turn raw data into actionable insights with:
Visual Tools: Genome-wide tracks, enrichment heatmaps, and peak distribution plots to simplify complex data.
Interactive Exploration: IGV tracks let you visualize peaks in real time, so you can dive deep into your results.
Curated Reports: Detailed summaries with annotations, pathway results, and differential analysis—making it easy to interpret the biological significance of your findings.
Every step of our process is built to deliver clarity and confidence, so you can focus on what matters most: advancing your research.
Applications
Your Experience-Focused Applications
cfChIP-seq offers a wide range of applications for researchers across various fields, enabling you to uncover critical insights into gene regulation and transcriptional activity. Here's how cfChIP-seq can empower your research:
1. Cancer Epigenomics
In the field of cancer research, cfChIP-seq provides powerful tools to study tumor progression, metastasis, and resistance mechanisms. By analyzing histone modifications from cfDNA, you can:
Classify Cancer Subtypes: Identify specific epigenetic signatures associated with different cancer types, aiding in the classification of tumors.
Track Tumor Evolution: Monitor how histone modifications change during tumor progression, providing insights into genetic instability and therapeutic response.
Study Resistance Mechanisms: Analyze the dynamic changes in epigenetic markers related to drug resistance, helping you explore new avenues for targeted therapy.
2. Transplant and Organ Biology
Transplantation research often requires precise monitoring of immune responses and graft health. cfChIP-seq enables you to:
Track Donor vs. Recipient Signals: Study the epigenetic changes in donor and recipient cells to assess the likelihood of graft rejection or acceptance.
Evaluate Graft Function: Assess the functional status of transplanted organs by analyzing histone modifications, which reflect the epigenetic response of both the graft and host cells.
Understand Immune Response: Investigate how immune cells react to transplant tissues, which can inform better immunosuppressive strategies.
3. Cardio and Hemato-scientists
cfChIP-seq is also invaluable in cardiovascular and hematological research, providing an in-depth look at the epigenetic regulation of gene expression related to heart and blood disorders. Key applications include:
Myocardial Damage Detection: Track epigenetic changes in response to myocardial injury, helping in early detection of cardiac events.
Hematologic Changes: Investigate the impact of blood disorders on gene expression, identifying potential biomarkers for disease progression or therapeutic targets.
4. Basic Epigenetic Research
Beyond disease-focused applications, cfChIP-seq is an essential tool for basic research in epigenetics:
Map Transcription Factor Binding Sites: Analyze the binding sites of key transcription factors in cfDNA, providing a clear picture of transcriptional regulation.
Study Developmental Changes: Examine how histone modifications vary during different stages of development, offering insights into cellular differentiation and gene activation.
5. Other Applications
From rare disease research to personalized medicine, cfChIP-seq can also be applied in various other research areas, such as:
Immuno-Oncology: Assess the immune system's response to cancer therapies through chromatin changes.
Gene Therapy: Monitor epigenetic changes in response to gene editing technologies like CRISPR.
Service Workflow
How We Partner with You
At CD Genomics, we treat every project as a collaboration, ensuring we meet your specific research needs with high-quality, personalized service.
1. Custom Study Design
We start by understanding your research goals. Whether you're focused on cancer, immunology, or organ-specific research, we customize our cfChIP-seq protocols to fit your exact needs. We'll also help you select the best antibodies for your study to ensure the most relevant histone modifications are analyzed.
2. Quality Control at Every Step
We ensure the highest quality results with clear checkpoints:
Sample Assessment: We verify the quality of your plasma or cfDNA before proceeding.
Continuous Monitoring: Data quality is monitored throughout the workflow to guarantee accurate outcomes.
3. Actionable Results
Our results aren't just data—they're insights:
Visual Reports: You'll receive easy-to-understand visual reports, including heatmaps and genome tracks, to simplify interpretation.
Comprehensive Analysis: Along with raw data, we provide detailed reports that include pathway analysis and gene annotations, giving you all the information you need to make informed decisions.
4. Ongoing Support
We're with you throughout the process:
Consultation: We discuss your study design and goals before we start to ensure clarity.
Data Interpretation: After generating your results, we assist in interpreting the data and provide guidance on how to use it in your research or publications.
Technical Support: We're available for follow-up consultations and offer support as your research progresses.
Quick Workflow Summary
Here's a quick look at how the cfChIP-seq process works, from sample submission to results delivery:
Bioinformatics
Bioinformatics Analysis – Comprehensive Data Interpretation
Our bioinformatics analysis ensures that your data is processed and interpreted with the highest level of precision, providing you with valuable insights into histone modifications and their biological significance.
Step
Description
1. Raw Reads Processing & Quality Control
Adapter trimming and quality filtering to ensure clean and high-quality reads.
2. Genome Alignment
Aligning the processed reads to the reference genome to identify the locations of histone modifications.
3. Peak Calling
Identifying enriched regions (peaks) where histone modifications are most prominent.
4. Peak Annotation
Annotating the peaks to determine their genomic locations, such as promoters, enhancers, and gene bodies.
5. GO Pathway Analysis
Mapping the annotated peaks to Gene Ontology (GO) terms to understand their biological functions.
6. KEGG Pathway Analysis
Linking the peaks to KEGG pathways to explore the molecular pathways affected by histone modifications.
7. Motif Analysis
Identifying enriched motifs within the peaks to determine potential transcription factor binding sites.
8. Differential Peak Analysis
Comparing peaks between groups to identify differences in histone modifications and correlating them with biological changes.
Sample Requirements
Ideal Sample Input
Sample Type
Plasma / cfDNA Extraction (1-2 mL plasma or 5-10 ng cfDNA)
