Fig. 4: In vivo validation of baseline JAK-STAT signaling in homeostasis.
From: JAK-STAT signaling maintains homeostasis in T cells and macrophages
a, Spatial transcriptomics profiles of spleens from wild-type and STAT1 knockout mice, shown for samples collected after in vivo cell fixation using formaldehyde. First row: hematoxylin and eosin (H&E) stains highlighting the anatomical structures of the spleen. Second row: spatial transcriptomics profiles annotated with gene expression clusters. Third and fourth row: expression levels of the T cell marker gene Cd8a and the macrophage marker gene Cd33 in the spatial transcriptomics data (scale bars, 1 mm). b, Violin plots showing the expression of STAT1-driven genes (top-15 downregulated genes comparing STAT1 knockout and wild type based on the RNA-seq data) and housekeeping genes (Actb, Hprt and Ubc) in the spatial transcriptomics data. c, Violin plots showing the expression of the ISGs Oas3, Ifit3 and Ifit1 in Cluster 4 of the spatial transcriptomics data. d, Representative RNA-FISH images for the ISG Oas3 (yellow) and the T cell marker gene Cd3e (dark blue) in spleen samples from wild-type and STAT1 knockout mice (scale bar, 50 µm). Autofluorescence of the red pulp is visible in magenta. e, Representative RNA-FISH images for the ISG Ifit3 (yellow) and the T cell marker Cd3e (dark blue) in spleen samples from wild-type and STAT1 knockout mice (scale bar, 50 µm). Experiments comprised two mice (a–c) or three mice (d and e) as biological replicates. Box plots (b and c) show the full data range, with the box indicating the interquartile range and median.
