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Rodent models have been extensively used to study mechanisms underlying post-traumatic stress disorder (PTSD), a complex mental health disorder which can often be directly linked to a traumatic event or events. Previous research suggests that in humans Apolipoprotein E (APOE) genotype may influence the susceptibility to develop PTSD as well as ensuing symptom severity. Apolipoprotein E is of particular interest due to its association with cognitive health and its role in cholesterol transport and metabolism, which may underlie its association with PTSD. Here, we describe a liquid chromatography and gas chromatography method to measure levels of cholesterol and related metabolites in small amounts of mouse tissue. Specifically, we provide methods to measure cholesterol and related metabolites in the brains of targeted replacement mice that express human E2, E3, or E4 under the control of the murine …