Cell-cycle-resolved analysis of RNA expression in neuroblastoma cells upon MYCN knockdown. Homo sapiens

Previous studies of c-MYC or MYCN effects on the cellular transcriptome have been performed with unsynchronized tumor cell populations. We reasoned that these results might have been influenced by different cell-cycle profiles of cells with high or low MYC levels as the expression of a large part of the genome varies with cell-cycle phase. To correct for this potentially confounding effect, we performed RNA sequencing in cell-cycle-synchronized neuroblastoma cells and then compared the transcriptomes of cells with high and low MYCN in equivalent cell-cycle phases. Overall design: IMR5/75 neuroblastoma cells with tetracycline-inducible MYCN shRNA were arrested at G1:S transition by thymidine treatment for 18 h. After washout, transcriptome was measured at 11 time points over 22h (2 biological replicates).