To assess the impact of hypoxia on global gene expression of beta cells, we performed bulk RNA-seq on mouse islets, human islets and MIN6 cells. Bhlhe40 was transcriptional repressor which was highly induced by hypoxia in beta cells. Thus, we established Bhlhe40 overexpressing MIN6 cells and performed RNA-seq to identify the targets of Bhlhe40. Overall design: Comparative gene expression profiling analysis of RNA-seq for human islets, mouse islets and MIN6 cells cultured in normoxic or hypoxic condition . Comparative gene expression profiling analysis of RNA-seq for MIN6 cells with or without Bhlhe40 overexpression.