Differential gene expression analysis of MYCN-amplified neuroblastoma cells after Doxycycline inducible shRNA knockdown of JMJD6 gene expression

JMJD6 oncoprotein induces neuroblastoma and exerts its biological effects through modulation of downstream target genes. We identified that JMJD6 knockdown reduces neuroblastoma cell proliferation, so we investigated which downstream signaling pathways were regulated by JMJD6. We performed Affymetrix Clariom S microarray experiments in stable Doxycycline inducible Control shRNA, and 2 independent JMJD6 shRNA CHP134 neuroblastoma cells after Doxycyline treatment for 40 hours. The Control shRNA, JMJD6 shRNA-1 (repeats A, B, C and D) and JMJD6 shRNA-2 samples (repeats A, B, E and F)were run four times. Differential expression analysis (DOXJ2 - NTJ2)-(DOXscr - NTscr) was done for each independent JMJD6 shRNA. The following are identical CEL file pairs: CHP_NT_shSCR_A_(Clariom_S_Human).CEL and CHP_NT_shSCR_A_dup(Clariom_S_Human).CEL, CHP_DOX_shSCR_A_(Clariom_S_Human).CEL and CHP_DOX_shSCR_A_dup(Clariom_S_Human).CEL, CHP_NT_shSCR_B_(Clariom_S_Human).CEL and CHP_NT_shSCR_B_dup(Clariom_S_Human).CEL, CHP_DOX_shSCR_B_(Clariom_S_Human).CEL and CHP_DOX_shSCR_B_dup(Clariom_S_Human).CEL. Affymetrix Clariom S microarray experiments were also performed in stable Doxycycline inducible Control shRNA, and JMJD6 shRNA-2 SKNAS neuroblastoma cells after Doxycyline treatment for 40 hours.