1 Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3G 1Y6, Canada.
2 Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC H9X 3V9, Canada.
3 PERFORM Center, Concordia University, Montreal, QC H4B 1R6, Canada.

In the field of epigenetic inheritance, delineating molecular mechanisms implicated in the transfer of paternal environmental conditions to descendants has been elusive. This protocol details how to track sperm chromatin intergenerationally. We describe mouse model design to probe chromatin states in single mouse sperm and techniques to assess pre-implantation embryo chromatin and gene expression. We place emphasis on how to obtain high-quality and quantifiable data sets in sperm and embryos, as well as highlight the limitations of working with low input. For complete details on the use and execution of this protocol, please refer to Lismer et al. (2021).