Fig. 3: CC030/GeniUnc mice have more numerous and transcriptionally distinct ILC2s at baseline compared to C57BL/6J. | Nature Communications

Fig. 3: CC030/GeniUnc mice have more numerous and transcriptionally distinct ILC2s at baseline compared to C57BL/6J.

From: Genetic diversity of Collaborative Cross mice implicates FFAR3 as a target for ILC2 anti-inflammatory reprogramming

Fig. 3

A Gating strategy to define ILC2s in strain comparison studies (pre-gated on viable, singlet leukocytes). B ILC2s as percentage of live lung cells and as (C) total ILC2s in lungs of C57BL/6J and CC030 mice without challenge (n = 6 per strain, combined from 2 independent experiments) (Bar height = mean, error bars = SD). D Representative flow plots of ST2 expression on ILC2s from C57BL/6J and CC030 lungs at baseline. E Quantification of ST2 expression on ILC2s in C57BL/6J and CC030 lungs at baseline. MFI = mean fluorescence intensity, FMO = fluorescence minus one control (n = 6 per strain, combined from 2 independent experiments) (Bar height = mean, error bars = SD). F Diagram for comparison of C57BL/6J and CC030 ILC2s by bulk RNA-sequencing (n = 3 per strain). G Quantification of differentially expressed genes in ILC2 between C57BL/6J and CC030. H Sample distance matrix. 0 = perfect identity, 500 = maximum distance. B6 = C57BL/6J, CC = CC030. I Principal component analysis plot of ILC2s from C57BL/6J and CC030 naïve lungs. Group-wise convex hulls are included in shading. J Bar plot representing annotated WikiPathways gene sets enriched in C57BL/6J compared to CC030. Gene sets were selected a priori as relevant to ILC2 signaling. K. Tree plot showing hierarchical clustering of the 30 Gene Ontology: Biological Processes (GO: BP) gene sets most enriched in C57BL/6J compared to CC030, ranked by normalized enrichment score. All adjusted p values for gene sets enriched in C57BL/6J are below 5 × 10−9. L Tree plot showing hierarchical clustering of the 30 Gene Ontology: Biological Processes (GO: BP) gene sets most enriched in CC030 compared to C57BL/6J, ranked by normalized enrichment score. The color of the circle for each gene set denotes the p value according to the scale underneath the figure. Significance for (B), (C), and (E) was assessed by two-tailed unpaired Student’s t-test. ****, p < 0.0001. Significance of gene set enrichment (J–L) was determined using a permutation-based one-sided test implemented in clusterProfiler (GSEA), with multiple testing correction by the Benjamini–Hochberg method (FDR).

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