scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection

Here, we establish a single-cell in vivo new RNA labeling sequencing method (scIVNL-seq) and apply it to survey time-resolved RNA dynamics during immune response to acute enteric infection with Salmonella. We show that the detection of new RNA synthesis reflects more realistic information on cell activation and gene transcription than total RNA level.

Interplay of RNA synthesis and degradation modulates the dynamics of total RNA. The bone marrow macrophages are first primed at a very early stage upon Salmonella infection. In contrast, the innate immune response of macrophages in intestine is limited.