EpiTect Hi-C

From QIAGEN, this kit provides a single-box solution for high-resolution mapping of chromatin folding, high-quality assembly of genome sequences, haplotype phasing, and identifying chromosomal rearrangements. It supports generation of Illumina-compatible NGS libraries from cross-linked cells in less than 2 days using a robust, simple and fast protocol with low cell input requirements. The procedure is a version of the in situ (in nucleus) Hi-C method in which nuclei are gently purified and permeabilized to maintain spatial organization of the genome during the initial digestion and ligation steps.

The assay works by purifying nuclei in which chromatin conformation is 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 identifies very large numbers of chimeric sequences derived from DNA strands that were closely associated in space, and quantification of ligation junctions enables determination of DNA contact frequencies. The kit can generate Hi-C NGS libraries from just 5000 cells, with sample input requirements reduced by one order of magnitude compared to published protocols. The protocol has been developed for work with cross-linked cells from mammalian cell cultures, and the workflow is completed in two parts over 1.5 days. Included Illumina adapters carry sequence bar codes that enable multiplex sequencing of up to 6 samples.

QC metrics evaluated from sequencing results of more than 40 EpiTect Hi-C libraries show that, on average, the generated NGS libraries far exceed criteria normally considered sufficient for a successful Hi-C experiment. Data analysis is available through the QIAGEN GeneGlobe Data Analysis Center, with the EpiTect Hi-C Data Analysis Portal providing QC sequencing reports, Hi-C contact matrices and visualization of chromatin contact maps.