Fig. 3: Different genes harbor various mRNA metabolic control strategies during immune response in macrophages.
From: scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection
A Numbers of genes that upregulated (log2 (fold change) > 0.25, p value < 0.05, Wilcoxon Rank Sum test) in new RNA and total RNA in macrophages at the indicated time points after infection compared with 0 h. B Ridgeline plot of new and total RNA expression correlations in macrophages. Genes highly expressed at the indicated time points were selected for Spearman’s rank correlation analysis of new and total RNA. C Scatter diagrams showing NTR and fold change of new RNA in infected macrophages to new RNA in uninfected macrophages (top); total RNA expression and fold change of total RNA in infected macrophages to total RNA in uninfected macrophages (bottom). Red spots indicate upregulated genes (log2(fold change) > 0.25); blue spots indicate downregulated genes (log2(fold change) < −0.25); grey spots indicate no change. D Heatmap of new and total RNA expression pattern in macrophages at the indicated time points. Genes highly expressed at each time point were selected and ordered into 8 clusters by their total RNA expression patterns, and rank of genes was mapped to new RNA. Expressions were scaled. E Heatmap showing enrichment scores of selected GO pathways in new RNA and total RNA at each time points post infection. F Line graph showing new and total RNA expression (upper) and new RNA transcription rate (α, normalized RNA counts per cells/h) and RNA half-life (t1/2, h) (lower) of Il1b, Ccl4 and Psmb9 at each time point in macrophages. G Dot plot showing average new RNA transcription rate (α) and RNA half-life (t1/2) of genes in GO pathways in macrophages. Genes significantly upregulated at 6 h or 72 h compared to 0 h were selected for GO enrichment analysis. Average values of α and t1/2 of these upregulated genes in the indicated GO were calculated and shown in the dot plot. Each dot shows an average value of α and t1/2 in a GO. The size of each dot represents the number of genes in the GO term. Source data are provided as a Source Data file.
