Capture Hi-C Service – High-Resolution Targeted Chromatin Interaction Mapping

When your research demands clarity at the regulatory level, Capture Hi-C offers the precision and efficiency you need. By targeting only your regions of interest, this approach delivers richer, cleaner interaction maps while saving sequencing resources.

At-a-Glance Advantages:

• Sharper Focus: Resolve chromatin loops at 1–2 kb scale, even in complex or repetitive genomic contexts.
• Smarter Data Use: Achieve deeper coverage in key regions with significantly reduced sequencing requirements.
• Custom-Fit Design: From genome-wide promoter panels to specific SNP loci—tailored to your research question.
• Cleaner Signals: Minimized background noise compared to whole-genome Hi-C, improving loop detection confidence.
• Integration Ready: Designed to work seamlessly alongside ATAC-seq, CUT&Tag, and other epigenomic assays for comprehensive analysis.

1. Define Your Target Regions

You identify the genomic loci of interest—such as promoters, SNP regions, or regulatory elements—and share your research goals with our technical team.

2. Custom Probe Design & Synthesis

We create a tailored probe panel to enrich your chosen regions. The scale can range from a few loci to genome-wide promoter coverage, with designs optimized for specificity and efficiency.

3. Hi-C Library Preparation & Probe Hybridization

Your samples undergo the Hi-C protocol, after which the library is hybridized with your custom probes to selectively capture interaction fragments from the target regions.

4. Targeted Sequencing

The enriched library is sequenced at a depth that ensures robust coverage of your targets while minimizing unnecessary data generation.

5. Data Analysis & Reporting

Our bioinformatics pipeline processes the data—detecting loops, annotating interactions, and integrating with relevant genomic features—so you receive results that are directly relevant to your study.

High-quality sequencing data is only the beginning. Our specialized bioinformatics pipeline transforms raw reads into meaningful biological insights, giving you a clear view of the 3D regulatory landscape in your target regions.

Our Analysis Workflow Includes:

• Data Quality Control – Filtering and trimming raw reads, removing adapters, and assessing library complexity to ensure reliable downstream results.
• Read Mapping & Filtering – Aligning reads to the reference genome, removing duplicates, and retaining only valid interaction pairs.
• Loop Detection & Interaction Calling – Identifying statistically significant chromatin loops within your targeted capture regions, using algorithms optimized for Capture Hi-C data.
• Functional Annotation – Linking interaction anchors to genomic features such as promoters, enhancers, and SNPs for biological interpretation.
• Variant–Gene Mapping – For GWAS or variant studies, mapping noncoding SNPs to potential target genes via loop connections.
• Data Visualization – Generating interaction heatmaps, arc diagrams, and genome browser tracks for direct integration into publications or further analysis.
• Multi-Omics Integration (Optional) – Overlaying Capture Hi-C loops with ATAC-seq, CUT&Tag, or ChIP-seq data to create a richer regulatory network model.

Our goal is to provide you with clean, well-annotated datasets that can be directly applied to hypothesis testing, figure preparation, or downstream computational modeling.