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Objectives : The purpose of this investigation was to evaluate the effects of Coptidis chinesis FRANCH. on the alteration of gene expression in a hypoxic model using cultured rat cortical cells. Methods : E18 rat cortical cells were grown in neurobasal medium containing B27 supplement. On 12 DIV, water extract from Coptidis chinesis FRANCH. was added (20 ㎍/㎖) to the culture media 4 hrs. On 14 DIV, cells were given hypoxic insult (2% O2/5% CO2, 37 ℃, 3 hrs), returned to normoxia and cultured for another 24 hrs. Total RNA was extracted from Coptidis chinesis FRANCH. treated and untreated cultures and alterations in the gene expression were analysed by microarray using rat 5K-TwinChips. Results : Effects on some of the genes whose functions were implicated in neural viability were as follows: the expression of apoptosis-related genes such as Clu (Global M = 1.3), of presynaptic inhibition's genes such as Penk-rs (Global M = 1.97), and of innate immuniti's such as Crp (Global M = 1.95), Defensin (Global M = 2.14), and Dnase1l3 (Global M = 1.57) increased. The expression of neurotrophic genes such as S100b (Global M = 1.42), and NFkB (Global M = 2.04) increased. Conclusions : Analysing the genes expressed on microarray, shows Coptidis chinesis FRANCH.protects cells by increasing viability and neural nutrition.