Dextran sulfate sodium (DSS) is widely used to induce experimental colitis in animal models, facilitating the investigation of inflammatory bowel disease (IBD). However, its strong polyanionic nature interferes with RNA extraction and suppresses reverse transcription and polymerase chain reaction (PCR) amplification, compromising downstream quantitative PCR (qPCR) analyses. Conventional RNA purification methods, such as lithium chloride precipitation and commercial kits, are limited by time, cost, and efficiency. This review outlines the key challenges associated with RNA isolation from DSS-treated tissues and presents an optimized extraction protocol integrating TRIzol with silica spin column purification. The method is systematically evaluated in mouse colonic tissues from DSS-induced colitis models, focusing on its compatibility with downstream qPCR analysis of pro-inflammatory cytokine expression.