Bioinformatic Analysis of Single-Cell Hi-C Data from Early Mouse Embryo

The adaptation of Hi-C protocols to enable the investigation of chromosome organization in single cells opens new avenues to study the dynamics of this process during embryogenesis. However, the analysis of single-cell Hi-C data is not yet standardized and raises novel bioinformatic challenges. Here we describe a complete workflow for the analysis of single-cell Hi-C data, with a main focus on allele-specific analysis based on data obtained from hybrid embryos.