Hi-C is a proximity ligation assay. It captures the three-dimensional organisation of chromatin in the nucleus. Crosslinked chromatin is digested, the cut ends are biotinylated, and the fragments are ligated in situ. The resulting chimeric fragments are sequenced. Read-pair frequencies between genomic loci represent spatial proximity. This produces genome-wide contact maps.
NGS - Next Generation Sequencing
Hi-C Library Preparation for Chromosomal Structure
Hi-C Library Preparation for Chromosomal Structure Analysis
These kits capture chromatin conformation across the whole genome, so you can detect structural variants by proximity ligation. Standard Hi-C kits deliver whole-genome contact frequency maps from your fresh or frozen cells and tissue, compatible with Illumina short-read sequencing.
Library preparation uses indexed adapter sets, which support dual-index multiplexing across your batches of samples. For structural variant detection or work with FFPE material, FFPE-compatible proximity ligation kits extend the assay to formalin-fixed tissue and do not require fresh cell input.
Capture Hi-C narrows the proximity ligation assay to the genomic regions you define. Custom capture modules are tiered by the number of capture targets you need and are available on request. All kits target Illumina short-read sequencing output.
- Scope of 3D mapping. For genome-wide contact frequency, a standard Hi-C kit gives you full coverage. For targeted regions or specific loci, a Capture Hi-C module scales to the number of target regions you need.
- Sample type. A standard Hi-C kit or combined capture-plus-library-prep bundle suits your fresh or frozen samples, while an FFPE-compatible Hi-C kit or FFPE-plus-library-prep bundle suits your fixed tissue.
- Library preparation included. A Hi-C kit without library prep covers your needs for capture reagents alone; the combined bundle adds library prep, and the FFPE bundle covers both for your fixed tissue.
- Multiplexing scale. Dual-index adapter sets support multiplexing of 16 to 32 samples from a single batch, and additional index sets let you expand multiplexing capacity further.
Applications
TAD and compartment mapping
Genome-wide Hi-C generates contact matrices defining topologically associating domains (TADs) and A/B compartments, linked to gene regulation.
Enhancer-promoter interaction mapping
Promoter Capture Hi-C focuses reads on promoter-anchored contacts, mapping distal regulatory interactions. Custom Capture Panels are available for your predefined genomic regions, such as regulatory loci or disease-associated variants. Pairing with ChIP-seq or CUT&RUN assay kits confirms occupancy.
Chromatin loop calling
High-resolution Hi-C data resolve CTCF-anchored loops and cohesin-mediated interactions. Chromatin looping tools let you engineer these interactions directly.
Structural variant detection
Hi-C contact maps identify large-scale chromosomal rearrangements, inversions, and translocations that reshape topological domains in cancer genomes.
Development and disease
3D genome changes accompany cell fate transitions, X-chromosome inactivation, and oncogene activation, tracked with epigenomic profiling kits.
FFPE clinical tissue
FFPE-compatible Hi-C chemistry extends 3D genome analysis to archival clinical specimens, linking chromatin topology to disease progression.
Product Catalog
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Hi-C Library Prep
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Capture Hi-C
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Hi-C Genome Assembly
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Hi-C Structural Variant Detection
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Frequently asked questions
Standard Hi-C generates contact maps across the whole genome. This requires deep sequencing to reach resolution at individual loci. Capture Hi-C uses biotinylated oligonucleotide probes to enrich for contacts involving target regions, such as all gene promoters. It concentrates sequencing depth on loci of interest at substantially lower cost per sample.
Genome-wide Hi-C at kilobase resolution for a human sample typically needs 1 to 2 billion read pairs. You can achieve lower-resolution compartment and TAD analysis with 100 to 500 million read pairs. Capture Hi-C reduces this requirement significantly by enriching target loci before sequencing.
Yes. FFPE-compatible Hi-C kits add extra DNA repair and reversal-of-crosslink steps to address formalin-induced damage. Library quality is generally lower than from fresh-frozen tissue. Check input mass and library quality carefully before proceeding to library prep.
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