b) RNAseq analysis (Salmon log2-transformed TPM values, z-score) of cultured intestinal fibroblast cell line Ccd18-co, stimulated with either TNF-α (100 ng/ml) or IL-1β (0.01 ng.ml) for 3 hours (n = 6 replicates per group, * P adjusted < 0.05 from DESeq2 ...
Price, M.N.; Dehal, P.S.; Arkin, A.P. FastTree 2—Approximately maximum-likelihood trees for large alignments.PLoS ONE2010,5, e9490. [Google Scholar] [CrossRef] [PubMed] R Core Team.A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Aus...
Price, M.N.; Dehal, P.S.; Arkin, A.P. FastTree 2—Approximately maximum-likelihood trees for large alignments.PLoS ONE2010,5, e9490. [Google Scholar] [CrossRef] [PubMed] R Core Team.A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Aus...
DESeq2 was used (DESeqDataSetFromMatrix) using default parameters, to carry out taxa differential analysis, results with a significance value cut-off of 0.05, adjusted for multiple comparisons, and fold-change of at least 2 were kept. Within taxa, differential analysis, to rank in terms of ...