Spatial gene expression in the mouse colon during experimental colitis measured with MERFISH

Gut inflammation involves contributions from immune and non-immune cells, whose interactions are shaped by the spatial organization of the healthy gut and its remodeling during inflammation. The crosstalk between stromal and immune cells is an important axis in this process, but our understanding has been challenged by incomplete cell-type definition and biogeography. To address this challenge, we used MERFISH to profile the expression of 940 genes in 1.35 million cells in colon slices collected across the onset and recovery from a mouse colitis model. We identified a large diversity of cell populations; charted their spatial organization; and revealed their polarization or recruitment in inflammation. We found a staged progression of inflammation-associated tissue neighborhoods orchestrated, in part, by multiple inflammation-associated fibroblasts, with unique expression profiles, spatial localization, cell-cell interactions, and healthy fibroblast origins. Similar signatures in ulcerative colitis suggest conserved processes in humans. Broadly, we provide a resource for understanding inflammation-induced remodeling in the gut and other tissues. 

Methods
This dataset was collected using multiplexed error robust fluorescence in situ hybridization (MERFISH) as described in the methods of the supporting paper. The methods section of this paper also describes the approaches used to analyze the data, which include the use of publicly available pipelines for the analysis of raw MERFISH images (github.com/ZhuangLab/MERFISH_analysis), RNA assignment to cells (github.com/kharchenkolab/Baysor), and single-cell analysis (github.com/scverse/scanpy). The organization of the provided files is described in the included README.md.