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Hi-C based Chromatin Interaction

Hi-C is a method designed to capture genomic configuration by combining probing proximity-based interactions and high-throughput sequencing. The method is based on chromatin crosslinking with formaldehyde, followed by digestion and re-ligation in a way that only fragments that are covalently linked will form ligation products. By sequencing these ligation products, it is possible to study the 3D organization of the genome. Hi-C enables studying the distribution of the portions of the genome that are lightly packed (A compartments, euchromatin) and more likely to be transcriptionally active, and the regions that are more tightly packed (B compartments, Heterochromatin). Hi-C can also be used to pinpoint Topologically Associated Domains (TADs), regions of the genome that have folded structures and are likely to have similar expression patterns, and to identify chromatin loops, DNA regions that are anchored together by proteins and that are often enriched in regulatory elements. BMKGene’s Hi-C sequencing service empowers researchers to explore the spatial dimensions of genomics, opening new avenues for understanding genome regulation and its implications in health and disease.

Service Details


Demo results

Featured publications

Service Features

● Sequencing on Illumina NovaSeq with PE150.

● Service requires tissue samples, instead of extracted nucleic acids, to cross-link with formaldehyde and conserve the DNA-protein interactions.

● The Hi-C experiment involves restriction and end repair of the sticky ends with biotin, followed by circularization of the resulting blunt ends while preserving the interactions. The DNA is then pulled down with streptavidin beads and purified for subsequent library preparation.

Service Advantages

● Optimal restriction enzyme design: to ensure a high Hi-C efficiency on different species with up to 93% valid interaction pairs.

● Extensive Expertise and publication records: BMKGene has vast experience with >2000 Hi-C sequencing projects from 800 different species and various patents. Over 100 published cases with an accumulative impact factor of over 900.

● Highly skilled bioinformatics team:  with in-house patents and software copyrights for Hi-C experiments and data analysis and a self-developed visualization data software.

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

● Comprehensive Annotation: we use multiple databases to functionally annotate the genes with identified variations and perform the corresponding enrichment analysis, providing insights on multiple research projects.

Service Specifications


Sequencing Strategy

Recommended data output

Hi-C Signal Resolution

Hi-C library

Illumina PE150

Chromatin loop: 150x

TAD: 50x

Chromatin Loop: 10Kb

TAD: 40Kb

Service Requirments

Sample type

Required amount

Animal tissue


Whole Blood




Plant- young tissue

1g/aliquot, 2-4 aliquotes recommended

Cultured Cells


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    Includes the following analysis:

    ● Raw data QC;

    ● Mapping and Hi-C library QC: valid interaction pairs and Interaction Decay Exponents (IDEs);

    ● Genome-wide interaction profiling: cis/trans analysis and Hi-C interaction map;

    ● Analysis of A/B compartment distribution;

    ● Identification of TADs and chromatin loops;

    ● Differential analysis on 3D chromatin structure elements among samples and corresponding functional annotation of associated genes.

    Cis and trans proportion distribution



    Heatmap of chromosomal interactions between samples



    Genome-wide distribution of A/B compartments图片23


    Genome-wide distribution of chromatin loops



    Visualization of TADs



    Explore the research advancements facilitated by BMKGene’s Hi-C sequencing services through a curated collection of publications.



    Meng, T. et al. (2021) ‘A comparative integrated multi-omics analysis identifies CA2 as a novel target for chordoma’, Neuro-Oncology, 23(10), pp. 1709–1722. doi: 10.1093/NEUONC/NOAB156.

    Xu, L. et al. (2021) ‘3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing’, Acta Pharmaceutica Sinica B, 11(10), pp. 3150–3164. doi: 10.1016/J.APSB.2021.03.022.

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