The present disclosure relates to compositions and methods for performing droplet-based high throughput sequencing upon genomic DNA of single cells (e.g., individual sperm). The instant disclosure provides a droplet that includes: i) a mammalian cell nucleus; and ii) a microbead presenting attached oligonucleotides, where the attached oligonucleotides include a nucleic acid sequence capable of hybridization and capture of genomic DNA and a microbead identification sequence that is common to all oligonucleotides attached to the microbead, where the mammalian cell nucleus is accessible to the microbead-attached oligonucleotides to an extent sufficient to allow for genomic DNA capture and amplification of genomic DNA to occur within the droplet.