Fig. 3: Spatial transcriptomics analysis of GALT.
From: Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue
a Hematoxylin and Eosin (H&E) staining of GALT in colon, along with the expression of B cell markers in spatial transcriptomics spots showing follicle location. b Manual classification of spots as subepithelial dome (SED) (black) or rest of follicle (white). c Heatmap of genes differentially expressed between SED and Follicle spots. d Expression of DNASE1L3 and complement components within the follicle, with spots coloured by expression and outlined as per classifications in (b). e Unsupervised clustering of spots using BayesSpace, with spots clustered based on gene expression and similarity to neighbouring spots. f Spots classified as lymphoid tissues (Cluster 7). g Sub-clustering of lymphoid tissue spots from (f) (GC = germinal centre). h Dot plot of gene expression within each subcluster, showing expression of cell lineage markers, DNASE1L3 and complement components. i Correlation matrix of DNASE1L3, complement components and genes associated with apoptosis in lupus, showing correlation of expression within the lymphoid tissue spots in (f). Correlations were calculated as Spearman correlation with pairwise p values corrected for multiple inference using Holm’s method, p values are detailed in Supplementary Fig. 3i. *P < 0.05; **P < 0.01; ***P < 0.001, ****P < 0.0001. Scalebars = 500 μm for (a, b, d), and 2 mm for (e, f and g). Source data are provided as a Source Data file.
