Fig. 2: New RNA is rapidly transcribed in BM macrophages post Salmonella infection.

A UMAP plot of CD45⁺ immune cells in BM and NTR at each time point post Salmonella infection. All cells from the indicated time points were combined to identify cell types (left). Ratio of new RNA to total RNA (NTR) was mapped onto UMAP plots (right). B New RNA imaging of femur sections (left) and mean fluorescence intensities (MFIs) of 5-EU labeled new RNA (right). New RNA was labeled with EU (red). Macrophages were stained with anti-F4/80 (green) antibody. Nuclei were counterstained with DAPI (blue). Scale bar, 50 μm. n = 5 biologically independent replicates. C RNA velocity flow projected in PCA space. Macrophages (left) or monocytes (right) from different time points were combined. Dynamo was used to quantify time-resolved RNA velocity. Cells are color-coded by time points. Streamlines represent integration paths connecting local projections from observed state to inferred future state. D Heatmap showing new RNA expression of genes with significantly up-regulated new RNA (fold change > 1.5; FDR < 0.05) in the main BM cell types. Expression levels were scaled. Mφ macrophage; Mono monocyte; Neu neutrophil; NK natural killer cell; DC dendritic cell; B B cell; T T cell. E New RNA and total RNA expression (log-normalized) of indicated genes from sample at 6 h after infection. F Flow cytometry showing IL-1β and TNF-α expression of BM macrophages (CD11b⁺CD11c⁻F4/80⁺) at indicated post-infection time points. Proportions of IL-1β⁺TNF-α⁺ macrophages to BM cells are shown (left). n = 6 biologically independent replicates. Results are shown as mean ± SEM. p values were determined by one-way ANOVA. G Functional scores (inflammatory response and defense response) of new RNA for each cell type at 6 h post infection. In the box plot, the lower and upper hinges are defined as the first and third quartiles. The center represents the median, and the whiskers extend from the hinges to the largest or smallest values within 1.5× the interquartile range. Data in (B) and (F) are representative of at least three independent experiments. Source data are provided as a Source Data file.