Extended Data Fig. 10. ILC2s are required for the goblet cell adaptation to the microbiota in the middle colon in the steady state.

a, Representative flow cytometric gating strategy for total ILC2s isolated from mouse MLN. b, Experimental schematic (created with BioRender.com) for ILC2 depletion (left) and gating strategy and summary (right) of ILC2s from MLNs in control and Cre+ mice. n=4 mice per group and summarize 2 independent experiments. Unpaired two-sided t-test. Data are presented as the mean +− s.e.m. c, Data summarizing the number of eosinophils recovered from colon regions A-D gated as in Extended Data Fig. 9c for SPF (purple) and GF (black) mice. n=22 mice from 7 independent experiments for SPF and n=9 mice from 3 independent experiments for GF. Box limits are the upper and lower quartiles with the middle line representing the median; and whiskers are 1.5 times the interquartile range from the box. d, Representative histograms showing expression of SIGLEC-F on the surface of eosinophils gated as in Extended Data Fig. 9c for SPF (purple) and GF (black) mice from colon region B. e, Data summarizing MFI of SIGLEC-F on eosinophils recovered from GF colon regions A-D gated as in c in SPF (purple) and GF (black) mice. n=21 mice from 7 independent experiments for SPF and n=9 mice from 3 independent experiments for GF. Box limits are the upper and lower quartiles with the middle line representing the median; and whiskers are 1.5 times the interquartile range from the box. f, Experimental schematic (created with BioRender.com) for eosinophil depletion via anti-IL-5 administration (top) and gating strategy and summary (bottom) of eosinophils from MLNs in isotype and anti-IL-5-treated WT SPF mice. n=4 mice per group; data summarize 2 independent experiments. Unpaired two-sided t-test. Data are presented as the mean +− s.e.m. g, Antibody staining of ANG4 protein (green; Minimum display value = 10 and maximum display value = 30) on colon tissue from isotype and anti-IL-5 treated SPF mice showing enrichment in the C2 region in all conditions. Nuclei are stained with DAPI (gray; Minimum display value = 0 and maximum display value = 150). n=2 mice per group and images representative of 2 independent experiments. h, Expression of example middle colon genes in Xenium colon samples (n=2 mice for each condition). i, Difference in cell counts assigned to the Xenium colon samples between DT treated ROSA26^LSL-DTR and Nmur1i^Cre-eGFPROSA26^LSL-DTR mice (t statistic with pooled variance). Colon samples were binned into four bins following the way single-cell data were generated along the unrolled X axis. Boxplots display first and third quartiles.