233 −1.0 −0.5 0.0 0.5 1.0 −2 −1 0 1 2 3 V1 V2 Location_rough ● ● colon ileum −1.0 −0.5 0.0 0.5 1.0 −3 −2 −1 0 1 2 3 V1 V2 Inflammation ● ● ● 1 2 3 −1.0 −0.5 0.0 0.5 1.0 −3 −2 −1 0 1 2 3 V1 V2 Diagnosis ● ● ● CD Control UC UC Non-IBD CD IBD-Inflamed Non-IBD IBD-non-inflamed Ileum Colon PC1 PC2 PC2 PC2 Extended Data Figure S7 Extended Data Figure S7 | Principal component analysis (PCA) plots demonstrating variation in cell type–enrichment labeled by diagnosis, biopsy inflammatory status and intestinal location. Each dot represents one tissue sample. Left: Patients with IBD, both CD and UC, show significantly different intestinal cell type composition compared to controls. Middle: Tissue inflammatory status induces shifts in cell type composition, showing differences between non-inflamed IBD tissue vs. control tissue and inflamed IBD tissue vs. control tissue. Right: Tissue location (ileum vs. colon) also demonstrates distinct variation in cell type composition. Mucosal host-microbe interactions in IBD
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