3C Sequencing (Hi-C Sequencing)

Hi-C sequencing, as known as chromosome conformation capture sequencing, short for 3C-Seq, is a next-generation sequencing (NGS) based method for interpreting the interaction patterns among different DNA sequences, as well as providing high-resolution chromatin three-dimensional structure information.


Chromosomal conformation capture (3C) is changing our understanding of the spatial configuration of the genome. There are often two key points in speculating chromatin interactions: one is to generate high-resolution signals, and the other is to capture useful information from the background signals. 3C technology can be widely used in studying gene expression, chromatin spatial conformation, and chromatin interaction. 3C and its derived technologies follow the same basic rule: chromatin digestion and DNA reconnection, which gathers sequences that are spatially close together, even though they may be far apart on the genome. By analyzing the characteristics of these junctions, for example by sequencing, a detailed map of chromatin interactions can be obtained.


AccuracyCost-efficientBioinformatics AnalysisOne-stop Service
High resolution and highly fidelity conformation of chromatin.Cost-efficient solutions to meet the needs of various research requirements.Our integrated bioinformatics pipeline can be tailored to suit your project.Provides one-stop service for library construction, sequencing, sample QC and data analysis.

Project Workflow

Sample Preparation

1. Sample Preparation

DNA purification;
quality assessment and quantification.

Library Preparation

2. Library Preparation

DNA fragmentation;
library preparation.


3. Sequencing

Illumina HiSeq;
PE 50/75/100/150.

Data Analysis

4. Data Analysis

Visualize and preprocess results, and perform custom bioinformatics analysis.

Chromosome Conformation Capture Sequencing (3C-Seq)

Bioinformatics Analysis Pipeline

In-depth data analysis:

  • Gene expression analysis;
  • Chromatin spatial conformation analysis;
  • Chromatin interaction analysis.

Sample Requirements

Cell sample: 0.5×106
RNA sample (concentration ≥ 1 ng/µL, quantity ≥ 5 µg)
1.8 ≤ OD260/280 ≤ 2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0.
Please make sure that the RNA is not degraded nor contaminated.

Sample storage: RNA can be dissolved in ethanol or RNA-free ultra-pure water and stored at -80°C. RNA should avoid repeated freezing and thawing.

Shipping Method: When shipping RNA samples, the RNA sample is stored in a 1.5 mL Eppendorf tube, sealed with sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, full statistical analysis & alignments, custom analysis reports on customer request.


  1. Ramani V, Deng X, Qiu R, et al. Massively multiplex single-cell Hi-C. Nature methods. 2017;14(3):263-6.
  2. Williamson I, Berlivet S, Eskeland R, et al. Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization. Genes & development. 2014;28(24):2778-91.
  3. Stadhouders R, Kolovos P, Brouwer R, et al. Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions. Nature protocols. 2013;8(3):509-24.
  4. Lan X, Witt H, Katsumura K, et al. Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic acids research. 2012;40(16):7690-704.
* For Research Use Only. Not for use in diagnostic procedures.

Research Areas
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