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

Methods Mol Biol. 2021:2214:295-316. doi: 10.1007/978-1-0716-0958-3_20.

Abstract

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.

Keywords: Allele-specific analysis; Mouse preimplantation; Single cell; scHi-C.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Blastocyst / cytology*
  • Blastocyst / metabolism
  • Cell Cycle
  • Computational Biology / methods*
  • Embryo, Mammalian / cytology
  • Embryo, Mammalian / metabolism
  • Female
  • Male
  • Mice / embryology*
  • Mice / genetics
  • Single-Cell Analysis / methods*
  • Software
  • Workflow