This protocol is designed for a standardized and efficient procedure to homogenize mouse tissue, conducive for RT-QuIC analysis. The process involves treating samples with PBS mixed with Triton-X100, followed by homogenization using a prob-tip sonicator. Centrifugation is then employed to remove detergent-insoluble fraction, optimizing the tissue for subsequent
analysis. The use of Triton-X100, a mild detergent, ensures the release of alpha-synuclein aggregates, enhancing signal specificity without compromising structural integrity. The protocol's significance lies in addressing the critical need for a reliable method in preparing mouse tissue for RT-QuIC analysis, with the distinct signal generated in assays validating its efficacy.