RNA-seq transcriptome analysis in naïve and TNF-a-treated Sirt6-silenced YAMC cells to enrich for direct Sirt6 targets associated with inflammatory stimulation.. Mus musculus

By comparing Sirt6-silenced YAMC cells to siControl-transfected YAMC cells, we found that there were 916 and 1,026 differentially expressed genes in the naïve and TNF-a treatment conditions respectively. We also found that there were 302 genes that were co-expressed differentially in both naïve and TNF-a treatment conditions between Sirt6-silenced and siControl-transfected YAMC cells. Overall design: YAMC cells were transfected with Sirt6 siRNA (siSirt6, 50 nM) and negative control siRNA (siControl, 50 nM) respectively using lipofectamine 2000. Forty-eight hours after transfections, the cells were cultured with medium containing TNFa (100 ng/mL) and medium alone respectively for additional 24 h. At the end of treatments, cells were harvested for RNA extraction followed by RNA-seq transcriptome analysis.