Get a Quote
quote
Get a Quote
×
Quote Request

Single-Nucleus Hi-C (sn-Hi-C) Service

Profile the 3D genome of frozen tissues and hard-to-dissociate samples with our Single-Nucleus Hi-C (sn-Hi-C) Service. By targeting isolated nuclei instead of whole cells, we overcome the limitations of tissue dissociation, enabling high-resolution chromatin conformation analysis on biobanked specimens, brain tissue, and multinucleated fibers (RUO).

  • Frozen Tissue Compatible: Perfect for archived clinical samples and biobanks.
  • Complex Tissue Ready: Optimized for brain, heart, and muscle where cell isolation is difficult.
  • Reduced Dissociation Bias: Nuclei extraction minimizes stress-induced transcriptional artifacts.
Unlock Frozen Samples

Workflow comparison showing how sn-Hi-C enables analysis of frozen and complex tissues by isolating nuclei

Overview: Unlocking Frozen & Complex Tissues

For years, single-cell 3D genomics was limited to fresh, easily dissociable samples. Standard Single-Cell Hi-C requires intact, viable cells, making it impossible to analyze archived clinical biobanks (frozen tissue) or complex tissues like the brain, where enzymatic dissociation destroys the delicate cellular architecture (e.g., neuronal dendrites) and often results in high cell death rates.

Our Single-Nucleus Hi-C (sn-Hi-C) Service bypasses these limitations by targeting the nucleus rather than the whole cell. By isolating intact nuclei from flash-frozen or difficult-to-dissociate tissues, we enable high-resolution chromatin conformation profiling on samples that were previously inaccessible.

Whether you are studying neurodevelopment in post-mortem brain tissue, analyzing tumor heterogeneity in archived patient samples, or investigating multinucleated muscle fibers, sn-Hi-C provides a robust solution to map TADs, compartments, and loops at the single-unit level. This capability is essential for correlating 3D chromatin state with historical clinical data in retrospective studies, opening new avenues for translational research.

(Note: This service is for Research Use Only. It is not intended for use in diagnostic procedures or clinical decision-making.)

Key Advantages

  • Archive Access: Unlock valuable insights from long-term frozen biobank samples.
  • Unbiased Sampling: Capture cell types that are lost during enzymatic digestion (e.g., fragile neurons).
  • Stress-Free: Mechanical nuclear extraction prevents transcriptomic stress responses.
  • High Fidelity: Preserves nuclear architecture in its native frozen state.

Applications: Where Cells Can't Go, Nuclei Can

sn-Hi-C extends the frontier of 3D genomics to the most challenging and valuable sample types, allowing researchers to explore biology in systems previously deemed "too difficult" for single-cell analysis.

Neuroscience & Brain Mapping

The brain is notoriously difficult to dissociate into single cell suspensions without causing massive cell death or selecting only robust cell types (glia) over fragile ones (neurons). The sn-Hi-C Advantage: Nuclei isolation is mechanical (Dounce homogenization) and works perfectly on frozen brain tissue. This allows for the unbiased profiling of neuronal subtypes (e.g., Excitatory vs. Inhibitory) to reveal how chromatin folding directs synaptic connectivity and plasticity in specific brain regions, such as the hippocampus or cortex.

Clinical Biobank Samples

Millions of valuable patient samples are stored as flash-frozen tissue in biobanks. The sn-Hi-C Advantage: You don't need to recruit new patients for fresh biopsies. sn-Hi-C unlocks retrospective studies, allowing you to link 3D genome reorganization to clinical outcomes using existing frozen cohorts. This is particularly relevant for studying epigenetic shifts in solid tumors where heterogeneity drives drug resistance.

Skeletal Muscle & Heart

Cardiomyocytes and skeletal muscle fibers are often large, irregularly shaped, or multinucleated, making standard single-cell sorting impossible. The sn-Hi-C Advantage: By extracting and sorting individual nuclei, sn-Hi-C allows for the deconvoluted analysis of these tissues. This reveals the distinct regulatory landscapes of polyploid nuclei within the same fiber, shedding light on the mechanics of syncytial gene regulation.

Comparison: sn-Hi-C vs. Standard scHi-C

The critical difference lies in the input material. If your samples are frozen, sn-Hi-C is the only viable option. While standard scHi-C offers excellent results for fresh cultures, sn-Hi-C provides versatility for complex tissues.

Feature sn-Hi-C (Nuclei) Standard scHi-C (Whole Cell)
Sample State Frozen or Fresh Fresh Only (High Viability Required)
Tissue Compatibility High (Brain, Heart, Muscle, Adipose) Low (Limited to blood/dissociable tissues)
Dissociation Bias Low (Mechanical extraction is unbiased) High (Enzymes may stress cells or select subpopulations)
Target Unit Intact Nuclei Intact Cells
Library Complexity Comparable to whole-cell Comparable to whole-cell

Our Workflow: From Tissue to Nuclei to Contacts

Our sn-Hi-C workflow combines precise nuclear extraction with sensitive low-input library preparation. Every step is optimized to maintain the 3D integrity of chromatin within the nuclear envelope.

Step 1: Nuclei Extraction & QC
We utilize optimized Dounce homogenization protocols to release nuclei from frozen tissue. This mechanical process gently breaks the cell membrane while maintaining nuclear envelope integrity. Nuclei are washed to remove cytoplasmic debris, stained with DAPI, and inspected microscopically for quality to ensure no clumping or damage.

Step 2: In Situ Hi-C & Sorting
Chromatin is fixed in situ within the isolated nuclei using formaldehyde. The DNA is then digested (typically with DpnII) and re-ligated to capture 3D contacts. Following this, we use Fluorescence-Activated Cell Sorting (FACS) to deposit single nuclei into individual wells of a 96-well or 384-well plate. Gating strategies are strictly set to select DAPI-positive singlets, avoiding doublets or debris.

Step 3: Library Prep & Sequencing
We generate sequencing libraries from each sorted nucleus using a specialized low-input protocol. This involves reversing crosslinks, fragmenting DNA, and amplifying the library with unique indexes. Libraries are sequenced (PE150) to sufficient depth to reconstruct single-nucleus contact maps. For higher throughput needs, this can be combined with combinatorial indexing strategies (see sci-Hi-C).

Schematic comparing cell isolation vs nuclei isolation for sn-Hi-C

Sample Requirements

sn-Hi-C is designed for challenging samples, but proper preservation is key. Flash freezing is essential to prevent ice crystal formation that could damage nuclear structure.

Sample Type Minimum Input Preferred Input Key Notes
Frozen Tissue 20 mg 50 - 100 mg Flash frozen in liquid Nitrogen is critical. Do not use OCT embedded tissue.
Complex Tissue 20 mg 50 mg Valid for Brain, Heart, Kidney, Muscle, etc.
Sorted Nuclei 10,000 nuclei 50,000 nuclei If providing suspensions, nuclei can be FACS sorted into plates or tubes.

Demo Results: High-Resolution Nuclear Maps

Figure 1: Cell-Type Specificity from Frozen Tissue

sn-Hi-C allows us to peer inside the nuclei of specific cell types harvested from heterogeneous tissues.

  • The Data: Single-nucleus Hi-C contact maps derived from a frozen mouse cortex sample.
  • Left Panel (Excitatory Neuron): The heatmap reveals specific TAD boundaries and loop anchors associated with neuron-specific genes (e.g., Neurod1).
  • Right Panel (Inhibitory Neuron): A distinct nucleus from the same tissue shows a different folding pattern, with alternate TAD structures silencing excitatory genes and activating inhibitory markers.
  • Conclusion: sn-Hi-C successfully resolves the structural heterogeneity of neuronal subtypes that would be lost in bulk tissue sequencing.

Single-nucleus Hi-C heatmaps distinguishing neuronal subtypes from frozen brain tissueFigure 1: Cell-Type Specificity from Frozen Tissue

Case Study: 3D Genome Reorganization in Single Nuclei

This landmark study demonstrated the power of sn-Hi-C to profile rare and fragile nuclear states.

The Challenge

Understanding how the 3D genome is reorganized during the oocyte-to-zygote transition is critical for developmental biology. However, mammalian oocytes and zygotes are extremely scarce (limited to a few cells per animal) and cannot be cultured in bulk for standard Hi-C.

The Solution

The researchers developed Single-Nucleus Hi-C (sn-Hi-C). They isolated individual nuclei from mouse oocytes and zygotes (both maternal and paternal pronuclei) and amplified the 3D contact information from these single units.

The Results

sn-Hi-C revealed that in the zygote, the paternal genome (derived from sperm) re-establishes TADs and compartments faster than the maternal genome. The data showed that the loss of higher-order structure in oocytes coincides with transcriptional silence, and the re-emergence of TADs in the zygote coincides with minor genome activation. Despite starting with single nuclei, the aggregated maps achieved resolutions comparable to bulk Hi-C.

Single-nucleus Hi-C data showing chromatin reorganization in oocytes and zygotes

The Conclusion

sn-Hi-C is a powerful tool for analyzing biological processes where sample quantity is limiting or where cells are too fragile for standard protocols.

Source: Flyamer, I.M., et al. "Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition." Nature (2017).

FAQ: Input & Resolution

References

  1. Flyamer, I.M., et al. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. Nature. 2017;544:110–114.
  2. Nagano, T., et al. Cell-cycle dynamics of chromosomal organization at single-cell resolution. Nature. 2017;547:61–67.
  3. Ramani, V., et al. Massively multiplex single-cell Hi-C. Nature Methods. 2017;14:263–266.
Leading Your Research Forward

Enhancing your vision research capabilities.

High-confidence 3D genomics services for chromatin interaction analysis and regulatory insight.

Quick Links
Contact Us
Copyright © CD Genomics. All Rights Reserved.
Top