Extended Data Fig. 6: Spatial characterization of DSS-induced inflammation over time.
From: Spatially restricted immune and microbiota-driven adaptation of the gut
a, Schematic of experimental design (n = 1 at each time point (created using BioRender (credit: H. Kang, https://biorender.com/l58o103; 2024). b, Recovery of DSS-disrupted gene expression across time. Genes that are differentially expressed (absolute log2 FC > 1) in the D12 DSS-treated mouse are shown. c, Top 10 Gene Ontology (GO) terms (Biological Processes) enriched for upregulated genes in each colon section of the D12 mouse compared to the sham (top 500 maker genes ranked by Wilcoxon test p-value; all have adjusted p-value < 0.05; enriched GOs are significant with adjusted p-value < 0.05 by Fisher’s exact test). d, Marker genes for each cluster shown in Fig. 3b (resolution = 0.3) obtained from colon samples across all time points. e, Expression of example marker genes for cluster 8 (Clca4b and Ido1) and cluster 10 (Il1b and Il11) in colon samples across all time points. White boxes indicate regions with residual expression at later time points. f, Volcano plot of DEGs comparing Ido1-positive spots (log transformed expression >2; Wilcoxon test) and Ido1-negative spots in cluster 8. g, Proximal (top), middle (middle), and distal colon (bottom) specific gene module scores plotted on swiss rolls at different stages of recovery.
