We report the application of ssequencing technology for high-throughput profiling of hypoxia cell in the yeast Cryptococcus neoformans. Our study represents the first detailed analysis of yeast transcriptomes in hypoxia 8 d compated with normoxia 8 d, stationnary phase and logarithmic phase, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA profiles in hypoxia. Overall design: Examination of hypoxia condition in one cell type and 4 different experimental conditions