Project description:Purpose: Explore IL-17B target genes expression via next-generation sequencing (NGS) in mouse lung tissues. Methods: Overexpress IL-17B in mouse lung tissues via intranasal injection of adenovirus encoding IL-17B (Adv-IL-17B) and empty virus (Adv-EV). Three days after infection lung tisses were removed for RNA collection. Five samples per group were mixed to one sample and used for next RNA purification. RNA samples were then used for high-throughput sequencing according to standard operation based on RNA Hiseq 4000. Results: Using an optimized data analysis workflow, we mapped about 13 million sequence reads per sample to the mouse genome (build mm10) and identified 269 upregulated and 99 downregulated genes in lung after IL-17B overexpression. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Altered expression of 20 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to lung inflammation and infection. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of IL-17B induced downstream genes with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based downstream genes characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Project description:Recombinant IL-17B (rIL-17B) promoted the sphere formation ability of CSCs in vitro and enhanced tumor growth and metastasis in vivo. Furthermore, the activation of autophagy was critically involved in IL-17B/IL-17RB-mediated regulation of CSC functions.
Project description:Compare the expression pattern of 17b-estradiol responsive genes in parent, OHT-resistant and ICI-resistant breast cancer cells. Keywords: 17b-estradiol responsive genes, OHT resistance, Fulvestrand resistance
Project description:YAP and TAZ are transcription cofactors implicated in the contractile and pro-fibrotic activation of fibroblasts. Fibroblast contractile function is important in alveologenesis, as well as in lung wound healing and fibrosis. As paralogs, YAP and TAZ may have independent or redundant roles in regulating transcriptional programs and contractile function. Using IMR-90 lung fibroblasts, microarray analysis and traction microscopy we tested whether independent YAP or TAZ knockdown alone was sufficient to limit transcriptional activation and contraction in vitro.
Project description:Here, we use a transcriptomic apprach to identify genes associated with variation in muscle contractile physiology differences among different muscles of the same individual.