Hi-C Sequencing Data Analysis

Hi-C Sequencing Data Analysis

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One of the Hi-C Sequencing Data Analysis service providers, CD Genomics uses bioinformatics to take you into the three-dimensional space of DNA based on the cutting-edge Hi-C sequencing technology. Our unique skills in data analysis will exceed our clients' expectations on personalized data analysis and provide the most comprehensive data analysis.

3D Structure Of Genome

At the nuclear level, chromosomes occupy specific areas (below). At the chromosomal level, Hi-C technology has revealed that chromatin can be divided into open and closed spaces, called "A" and "B" compartments. A compartment is closely related to accessible, transcriptionally active euchromatin, and B is associated with inaccessible, transcriptional silencing heterochromatin (see figure). With the increase of sequencing depth and resolution, the compartment is subdivided into topological domain (TADs). In the Hi-C experiment, TADs identification was mainly based on reduced interactions in the border areas (see figure). Within TADs, regulatory elements interact with regulatory genes to activate gene transcription. Histone H3K27ac and ATAC-seq can be used to identify active regulatory elements (see figure). TAD boundaries are stabilized by laminin complexes and are usually rich in CTCF and transposable elements or housekeeping genes; boundaries are essential for TAD to perform its normal function.

The 3D structure of genome. Fig 1. The 3D structure of genome. (Spielmann,M; et al.2018)

Hi-C Technology Introduction

Hi-C technology is derived from Chromosome Conformation Capture (3C) technology, which takes the entire cell nucleus as the research object, uses high-throughput sequencing technology, combined with methods in bioinformatics, to study the spatial location of the entire chromatin DNA throughout the genome. By capturing all DNA interaction patterns in chromatin, high-resolution chromatin three-dimensional structural information is obtained. Combining ATAC-seq, ChIP-seq, genome, transcriptome and other data, from gene regulation Networks and epigenetic networks, relevant mechanisms of organism trait formation can then be explained.

Possible strategies to interpret structural variations in the 3D genome. Fig 2. Possible strategies to interpret structural variations in the 3D genome. (Spielmann,M; et al.2018)

Information Analysis Content

Bioinformatics analysis includes standard analysis and advanced analysis

Standard analysis content

1. Sequencing quality assessment;

8. Interaction Atlas Construction;

2. Hi-C data quality control comparison statistics;

9. InDel detection and annotation;

3. Insert statistics;

10. TAD analysis;

4. NT library comparison;

11. Genomic heterozygosity statistics;

5. Aligning reference genomes;

12. 3D structure reconstruction;

6. Comparison and filtering;

13. Chromosome span haplotype construction

7. SNP detection and annotation;

14. Development of control elements.

Standard analysis content

1.Relationship between differential conformation and expression regulation by joint analysis with CHIP-SEQ.
2.Relationship between differential conformation and expression regulation by joint analysis with RNA-SEQ.
3.Joint analysis with GWAS to study the regulatory effect of SNP on long-distance non-linked regions.
4.Genome-wide Delta analysis.

How It Works

CD Genomics is a high-tech company specializing in multiomic data analysis. We provide services such as project design, data analysis, and database construction. With a focus on developing breakthrough products and services, we are a pioneer in the biotechnology industry, serving researchers and partners worldwide.

How It Works

CD Genomics provides general analysis and customized analysis of Hi-C Sequencing Data Analysis service. If you are interested in our services, please contact us for more detailed information.


  1. Spielmann,M; et al. Structural variation in the 3D genome[J]. Nature Reviews Genetics,2018 Jul;19(7):453-467.
* For Research Use Only. Not for use in diagnostic procedures.
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