Understanding the molecular interactions within the neuromuscular apparatus in the stomach is crucial for understanding their role in maintaining interstitial cells, such as the interstitial cells of Cajal (ICC), smooth muscle, and enteric neurons, as well as their contribution to gastric motility in both healthy and diseased states. Disruptions of these systems can lead to various gastric motor disorders and diseases, making it essential to explore their functions in detail. We herein present a protocol for gene knockdown using small interfering RNA (siRNAs) in organotypic culture. This ex vivo approach allows the precise manipulation of the gene expression in a tissue environment that closely mimics in vivo conditions, providing valuable insights into the gene function and its effects on gastric physiology. The protocol includes detailed steps for tissue preparation to ensure the preservation of the gastric muscles and the associated neuromuscular apparatus. We then describe the process of siRNA-mediated gene knockdown, offering tips for optimizing transfection efficiency and gene silencing. Additionally, we outline methods for analyzing the effectiveness of knockdown, including both quantitative and qualitative methods for the evaluation of the target gene expression. This protocol is adaptable to various research needs, allowing researchers to focus on specific genes of interest within the neuromuscular system of the stomach. By applying this approach, investigators can deepen their understanding of the molecular mechanisms underlying gastric motility and contribute to the development of new therapeutic strategies for treating gastric motor disorders and diseases.
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