Different fibroblast subtypes propel spatially defined ileal inflammation through TNFR1 signalling in murine ileitis

TNFΔΑRE mice represent a model for Crohn's Disease (CD) ileitis. We wanted to examine the cellular and trascriptional heterogeneity of immune and stroma cells (not including the epithelium) in the ileum of wild type and TNFΔΑRE mice. Intestinal samples were digested using a mix of Collagenase XI/ Dnase/ Dispase II after removing epithelial cells. To ensure sufficient representation of all the basic cellular compartments, especially given that stromal cells in TnfΔARE accounted for less than 10% of the total cell population, we sorted myeloid cells (CD45+CD11B/CD11C+), lymphoid cells (CD45+CD11B-CD11C-), and stroma cells (CD45-EPCAM1-), mixed them to an equal ratio.The scRNA-seq libraries were prepared following the 10X Genomics user guide Single Cell 3’ v3.1 reagent kits pooled and sequenced with the DNBSEQ-G400 sequencer (PE100) (BGI Genomics).