Optimized SYBR Green qRT-PCR Workflow for Pharmacologic Perturbation in Head and Neck Squamous Cell Carcinoma (HNSCC) Models (TR146 and SCC58) v1

This protocol details a standardized SYBR Green-based qRT-PCR workflow for assessing transcriptional responses to pharmacologic perturbations (e.g., 4NQO, BaP) in head and neck squamous cell carcinoma (HNSCC) lines (TR146 and SCC58). Unlike general qPCR methods, this workflow is optimized for comparative toxicology, emphasizing strict matched-vehicle controls, light-sensitive handling for polycyclic aromatic hydrocarbons (PAHs), and plate-level normalization. It utilizes theΔΔCtmethod with GAPDH normalization to quantify relative gene expression changes following DNA damage or AHR pathway activation.