Extended Data Fig. 5: RNA sequencing of AHR-deficient intestinal LEC.
From: Endothelial sensing of AHR ligands regulates intestinal homeostasis
a, Histogram overlays showing Cre efficiency and specificity in SI BEC (CD45−CD31+PDPN−; red) and LEC (CD45−CD31+PDPN−; green) from ECΔAhr mice treated with a full (5x) tamoxifen regimen (shaded histograms) comapred to tamoxifen-treated littermate ECWT controls. Grey bar shows negligable Cre+ cells within CD31− gate. Graphs show summary data (ECWT n = 24; ECΔAhr n = 29). b, Composition of immune cell subsets between ECWT and ECΔAhr mice during tamoxifen treatment (analysed day 7 of 14 day course, n = 5–7 mice/genotype). Immune cell subsets defined as in Extended Data Fig. 6a. c, Experimental setup and gating strategy for RNA sequencing experiments. 3h post-FICZ treatment, NuTRAP-reporter+ (mCherry-RanGAP1+eGFP-L10a+) BEC and LEC from SI and colon of ECΔAhr and ECWT controls were sorted by FACS and sequenced. d, Small intestinal LEC – expression of top 50 DE genes (based on adjusted p value) between ECΔAhr (Ahr-deficient) and ECWT (Ahr WT). e, Results of GSEA analysis of selected Hallmark pathways in ECΔAhr LEC, displayed as a barcode plot (NES, normalised enrichment score; FDR, false discovery rate). f, Venn diagram showing number of DE genes that overlap in BEC and LEC. g, Homeostatic proliferation: EdU detection following 2-week EdU feeding in WT and KO LEC from suboptimally-depleted ECΔAhr mice (n = 7 mice). Gating eample of WT and KO BEC and LEC selection (within total CD31+ gate) shown. h, VEGFA administration: EdU detection in ECΔAhr mice WT and KO LEC following 2-week VEGFA165 administration alongside EdU feeding (n = 9 mice). i, DC101-mediated blockade: EdU detection in ECΔAhr mice WT and KO LEC following VEGFR2 blockade with DC101 antibody (n = 7 mice), or control IgG alongside EdU feeding (n = 6 mice). *P < 0.05, **P < 0.01, ****P < 0.0001, as calculated by paired t-tests (g,i). or unpaired t-tests (i – WT-WT, and KO-KO comparisons only).
