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This protocol describes the process of isolating nuclei from human brain tissue using the CellRaft Array for single nucleus Whole Genome Amplification. In this process, 5000 nuclei were diluted in PBS then dropwise added to the CellRaft Array. To avoid cross contamination the collection wand was placed in tubes containing DNase-I diluted solution. Once deposited into the tube for scWGA, tubes are centrifuged and then samples are either stored at -80°C or processed for scWGA. The methodologies used for scWGA are PicoPlex method with and without nuclei immunostainging, and DAPI staining using dMDA or PTA.