GSE168253
Next Generation Sequencing Facilitates Quantitative Analysis of Murine Salivary Gland Transcriptomes at 8 and 32 weeks
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular functions. The goal of this study is to compare NGS-derived salivary gland transcriptome profilings (RNA-seq) to better understand the molecular changes in adult sublingual glands in the absence of the Nkx2.3 transcription factors. Methods: Female sublingual salivary gland mRNA profiles were generated by deep sequencing, in 4 replicates for Nkx2.3 knockout mice, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with STAR followed by DESeq2. Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm9) and identified 496 genes that were differentially expressed between the wildtype and Nkx2.3-knockout murine female sublingual salivary glands . RNA-seq data provided valuable insights into the nature of the functional differences resulting from the Nkx2.3 disruption Conclusions: Our study represents the first detailed analysis of sublingal salivary gland transcriptome profiling differences resulting from the Nkx2.3 disruption, with biologic replicates, generated by RNA-seq technology. Our results confirmed functions of many previously studied genes. We conclude that RNA-seq-based transcriptome characterization would offer a comprehensive and sensitive evaluation of the gene expression. Overall design: Female sublingual salivary gland mRNA profiles of 8- and 32-week old mice were generated by deep sequencing, in 4 replicates using Illumina.