Extended Data Fig. 1: Stroke induces long-term IgG loss in patients and shrinks PP in mice after ischemia-reperfusion injury.

a, Concentrations of plasma IgG in stroke patients after 1−3 d and 4−10 d of hospital admission and healthy controls measured by ELISA (n = 14−21 per group, ordinary one−way ANOVA, **P = 0.0037, ****P < 0.0001). b, Quantification of brain infarct volume after 24 h and 72 h of stroke (n = 9−12 per group). c, Quantification of plasma IgG in sham or stroke mice after 24 h, 72 h and 7 d using ELISA (n = 5−12 per group, ordinary one−way ANOVA, ****P < 0.0001). d, The total number of intestinal PP per mouse 24 h and 72 h after sham surgery or stroke or unoperated naïve mice (n = 8−13 mice per group, two−tailed Mann−Whitney U test, sham 24 h vs naïve P = 0.6883, sham 72 h vs naïve P = 0.5810, 24 h sham vs stroke P = 0.5597, 72 h sham vs stroke **P = 0.0047). e, Illustration of the intestinal tissue preparation for unstained−volume analysis of whole PP or whole−mount staining of B and T cells in PP, followed by tissue clearing and LSFM−based 3D volume analysis. f, Representative LSFM images of cleared unstained intestinal PP showing their shrinkage 24 h after sham or stroke, scale bar=500 µm. g, Tissue volume analysis of PP after 24 h and 72 h of sham or stroke; (n = 23 PP for sham and n = 16 PP for stroke, n = 3−4 mice for 24 h and n = 34 PP for sham and n = 24 PP for stroke, n = 6 mice for 72 h, two−tailed Mann−Whitney U test, naïve vs sham 24 h P = 0.3990, 24 h sham vs stroke **P = 0.0055, 72 h sham vs stroke ****P < 0.0001). h, Overview of the human−in−the−loop segmentation workflow for automated analysis of B cell follicles volume and T cell zone volume. Data represented as mean ±s.d., All data are combined from at least three independent experiments. PP=Peyer’s patches.