Extended Data Fig. 4: The steady state intestinal spatial landscape is robust.
From: Spatially restricted immune and microbiota-driven adaptation of the gut
a, Average log FC of gene expression comparing SPF and GF animals (absolute value > 0.1). Genes that are prevalent in SPF (top, expressed in >20% of the SPF but <20% of GF Visium spots) or GF (bottom, expressed in >20% of the GF but <20% of SPF Visium spots) were highlighted in color. b, Prevalence (% expressed per Visium spot) of genes in each region. Highlighted genes with high log2FC in expression between SPF and GF mice (absolute average log2 FC > 1). c, Dot plot of expression of select genes by region and condition. d-e, Expression of Mbl2 (d) and S100g (e) along the intestine of SPF, GF and FMT mice. Biological replicates are shown for each condition (SPF and GF, n = 3; FMT n = 2). f, Examples of genes that exhibit expression gradients along the unified X axis in the SI (Guca2a, top) and colon (Hmgcs2, bottom). g, Scatter plots showing the concordance (Pearson correlation, r) of spatial association (the Spearman correlation between the proximal-distal axis and gene expression) across biological replicates (n = 3 SPF, n = 3 GF, n = 2 FMT). Points show the spatial association of an expressed gene and lines represent the fitted linear regression curve. Examples shown in panel f are highlighted in the corresponding panels (circle - Guca2a; triangle - Hmgcs2). h, Expression of the circadian clock associated genes Nr1d1 and Per2 in the colon of SPF and GF mice measured during the light or dark cycle (n = 1 per condition). i, Scatter plots showing concordance of spatial association between animals studied during the light or dark cycle (n = 1 for each cycle). D, duodenum; J1, jejunum 1; J2, jejunum 2; I, ileum; C, colon; C1, proximal colon; C2, middle colon; C3, distal colon.
