Multiplexed Sequential DNA FISH in Caenorhabditis elegans Embryos

This protocol describes a high-throughput and multiplexed DNA fluorescence; in situ; hybridization method to trace chromosome conformation in; Caenorhabditis elegans; embryos. This approach generates single-cell and single-chromosome localization data that can be used to determine chromosome conformation and assess the heterogeneity of structures that exist; in vivo; . This strategy is flexible through modifications to the probe design steps to interrogate chromosome structure at the desired genomic scale (small-scale loops to whole-chromosome organization). For complete details on the use and execution of this protocol, please refer to Sawh et al. (2020).