RNA-seq Analysis of Transcriptomes in ß-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing aTC1-6 cells

Purpose: The goal of this study is to determine the molecular mechanisms involved in the NIK regulation of a cell function. Methods: mRNA profiles of ß-Gal control, NIK, and NIK(KA) overexpressed aTC1-6 cells were generated by deep sequencing using an Illumina Hiseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.89) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1). Conclusion: Our study represents the first detailed analysis of NIK-overexpressing aTC1-6 cell transcriptomes, generated by RNA-seq technology. Our results show that 328 genes were upregulated and 48 genes were downregulated following NIK overexpression. GO analysis indicated that the upregulated genes were primarily related to the immune response. KEGG pathway enrichment analysis showed that immune signaling pathways, including the TNF, NF-?B, and chemokine signaling pathways, were significantly activated by NIK overexpression in aTC1-6 cells, while genes related to metabolism-associated signal pathways were significantly decreased. NIK(KA), the dominant-negative mutant of NIK, does not affect gene expression in aTC1-6 cells. Overall design: mRNA profiles of ß-Gal control, NIK, and NIK(KA) overexpression aTC1-6 cells were generated by deep sequencing, in a single test, using Illumina