GSE201278
A novel strategy for regulating mRNA's degradation via interfering the AUF1's binding to mRNA [RNA-seq]
Purpose:To explore how JNJ-7706621 affected the cellular processes and the possible relationship between AUF1 functions, we analyzed global transcriptome alterations of SK-MEL-2 cells at certain time points (48 h) after JNJ-7706621 treatment using RNA-seq analysis. Methods: Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis. This choice is motivated by the decision to maximize the sensitivity of this analysis, in order to perform a massive screening and identify candidate genes to be validated with a wider sample population with real-time PCR analysis Results: The quantity of gene expression was calculated by FPKM (Fragments Per Kilobase of transcript per Million fragments mapped). Genes with log2 (Fold change) >1 and P value < 0.05 were considered as differentially expressed genes (DEGs).  There were 146 upregulated genes and 158 downregulated genes for a total of 304 DEGs that were results are shown in Fig. 8A. Furthermore, the enriched KEGG pathways were analyzed and the top 30 pathways involved in these 304 DEGs between the two groups are shown in Figure SI. Among the top 30 pathways, 9 pathways related to mitochondrial function had significant effects. 37 DEGs in KEGG pathway associated with mitochondrial function was conducted and analyzed. Conclusions: 70% gene was up-regulated by  JNJ-7706621 and up-regulated genes mainly affect cancer and inflammatory factors according the RNA-seq analysis Overall design: mRNA profiles of SK-MEL-2 cells (ctrl) and SK-MEL-2 cells (treated by JNJ-7706621)