Single cell genomic analysis has already impacted a range of life science fields, including tumor clonality, neuronal mosaicism, and drug resistance mechanisms. These methods rely on access to relatively fresh samples, ensuring that a maximum amount of high-quality nucleic acid can be extracted from a given cell. Conversely, translational research depends on the availability of human samples which are difficult to acquire in large numbers as fresh samples. As an alternative to single cell sequencing, single nucleus sequencing (SNS) has enabled genomic analysis using the plentiful cryopreserved samples found in various biobanks and other facilities. The CellRaft® Technology uniquely enables the sorting and isolation of single nuclei for downstream analysis. Here we provide optimal methods for imaging nuclei on CellRaft Arrays, and downstream molecular biology protocols for the amplification and preparation of nucleic acid prior to sequencing.