Gimenez-Llorente, DanielPortela, MartaLosada, AnaManzanares, MiguelAndreu, Maria Jose2024-05-092024-05-092023-04-30STAR Protoc. 2023 Apr 30;4(2):102267.http://hdl.handle.net/20.500.12105/19312Hi-C studies the three-dimensional structure of the genome by detecting genome-wide chromatin regions that are in spatial proximity within the nucleus. We developed single-blastocyst Hi-C in mutant mouse embryos to genotype them on sequence. We describe steps for embryo fixation and nuclei permeabilization, after which chromatin is digested and re-ligated having incorporated a biotin-labeled nucleotide at the ligation junction. After cross-link reversal, we then detail purification of immobilized chimeric DNA ligations, library generation, sequencing, and genome-wide analysis of interactions. For complete details on the use and execution of this protocol, please refer to Andreu et al. (2022).1.engVoRhttp://creativecommons.org/licenses/by-nc-nd/4.0/Attribution-NonCommercial-NoDerivatives 4.0 Internacional371264454210226710.1016/j.xpro.2023.1022672666-1667STAR protocolsopen access