Extended Data Fig. 7: Spatial transcriptomic analysis of IECs in response to acute nociceptor activation.
From: Neuro-epithelial circuits promote sensory convergence and intestinal immunity
a, Schematic of chemogenetic nociceptor activation for Xenium analysis. b, Overview of the Xenium-based spatial transcriptomics data structure. c, Overview of the processed Xenium data of mouse ileum with UMAP and all cell clusters colored by cell class. d, Gene expression for Epcam and top 5 marker genes per IEC population, determined by Wilcoxon rank-sum test. e, Visualization of CellCharter zones. f, IEC composition of CellCharter zones. g, Spatial embedding of IECs along the crypt-villus spatial axis. h, Crypt-villus axis distribution in each spatial zone, with IQR ranges as vertical dashed lines. i-j, IEC gene expression (i) and ISC-related gene expression (j) along the crypt-villus axis with epithelial global statistical analysis. Statistical significance of gene expression changes was determined via using a %ΔAUC threshold of ± 10. k, Visualization of Ramp1 gene expression in Xenium dataset. Scale bar=100 µm. l, CGRP receptor gene expression (Ramp1/Calcrl) along the crypt-villus axis with epithelial global statistical analysis. Shown images are representative of 3 biological replicates in each group from 1 independent experiment in k. The illustration in a was created in BioRender. Emanuel, E. (2025) https://biorender.com/b1xymo3.
