EpiTect Hi-C

• All-inclusive kit – quality-controlled reagents for generating Hi-C NGS libraries
• Included Illumina adapters with sequence bar codes for multiplex sequencing
• Fully tested, robust and fast protocol – Hi-C library generation in <2 days
• Low sample input requirement – libraries generated from just 5000 cells
• Data analysis pipeline based on open-source tools

Hi-C was originally conceived as a powerful technique for genome-wide chromosome conformation capture, enabling the characterization of chromatin folding at kb resolution. However, the technology also has other important applications. For example, Hi-C is used for generating highly contiguous genome assemblies, with few and very long scaffolds, from organisms without a known reference genome. In addition, Hi-C is also very useful for haplotype phasing and detection of chromosomal rearrangements.

The EpiTect Hi-C Kit offers a robust, yet simple and fast, protocol with low cell input requirements that enables generation of high-quality Hi-C Illumina NGS libraries from cross-linked cells in less than 2 days.

The EpiTect Hi-C Kit generates high-quality Hi-C NGS libraries, ensuring that first-rate data is generated from costly downstream deep sequencing. Sequencing results from more than 40 EpiTect Hi-C libraries have been analyzed to evaluate the performance of the kit. The most important QC metrics are shown in the following figures:  Percentage of Hi-C events,  Percentage of long-range cis interactions,  Cis/Trans ratio,  No strand orientation bias with the EpiTect Hi-C Kit and  Percentage of paired reads deriving from a single restriction fragment. The data show that the EpiTect Hi-C Kit generates NGS libraries that, on average, far exceed criteria normally considered sufficient for a successful Hi-C experiment.

Hi-C is a proximity ligation assay that captures chromatin interactions on a genome-wide scale. The EpiTect Hi-C Kit is a specialized DNA preparation resulting in an Illumina-compatible NGS library (see figures  EpiTect Hi-C workflow – day 1 and  EpiTect Hi-C workflow – day 2). Briefly described, the assay starts with the purification of nuclei in which chromatin conformation has been frozen by chemical cross-linking of DNA binding proteins and DNA. The DNA is then completely digested with a 4 bp restriction enzyme. Open DNA ends are labeled with biotin and subsequently ligated. Paired-end sequencing of the Hi-C ligation products identifies very large numbers of chimeric sequences that derive from DNA strands that were closely associated in space. The probability that two sequences are ligated together is a function of their average distance in space. Quantification of ligation junctions allows for the determination of DNA contact frequencies from which high-resolution mapping of chromatin folding can be achieved.