The Hypoxia-Inducible Factors induce the expression of the histone demethylases JMJD1A (KDM3A) and JMJD2B (KDM4B), linking the hypoxic tumor microenvironment to epigenetic mechanisms that may foster tumor progression. Using transcript profiling, we have identified genes that are regulated in RCC4 with siRNA-mediated knockdown of JMJD1A and JMJD2B. This dataset includes expression data obtained from renal cell Carcinoma being loss or mutation of the von Hippel-Lindau (VHL) tumor suppressor gene combination with siRNA-mediated knockdown of histone demethylases JMJD1A and JMJD2B. Overall design: 9 samples were analyzed. The log2-transformed normalized signal intensities were used for downstream pairwise comparisons (using Partek Genomic Suite): SiControl>SiJMJD1A; SiJMJD1A>SiControl; SiControl >SiJMJD2B ; SiJMJD2B>SiControl;