High-Throughput Preparation of Improved Single-Cell Hi-C Libraries Using an Automated Liquid Handling System

Hi-C is recognized as a gold standard approach to analyze the three-dimensional (3D) organization of chromatin or chromosomes on a genome-wide scale. It has revealed many characteristic features of structural organization and contributed to our understanding of how gene expression is related to the 3D organization of chromatin. However, the original Hi-C is designed to analyze the average structure across millions of cells, which makes the method unsuitable if the cell population of interest is not homogeneous or the purpose is to pursue the dynamic aspects of the structural features in individual cells. To overcome such limitations, we established single-cell Hi-C and have improved the method further in terms of data quality and throughput. Here we describe the revised single-cell Hi-C protocol, including the settings of the liquid handling system essential for increased throughput.