Fig. 2: Cellular microenvironments define the spatial architecture of Control and AKI kidneys.

A Zoomed in image of one field of view in the AKI sample: The cellular composition within a 30um radius around each cell is calculated, and these compositions are then clustered to create 17 distinct MEs. B Cellular composition within each ME is calculated as the relative mean abundance of each cell type. Barplot showing the relative frequency of each ME within the Control and AKI samples. Gray asterisk represents enrichment in control and blue enrichment in AKI (*p < 0.05; **p < 0.01 of a one-sided t test). Source data are provided as a Source Data file. C Spatial locations of five MEs in one representative control and one AKI sample. D Spatial locations of all injured PT cells in one AKI sample plotted in color over the locations of all cells belonging to ME-5 plotted in gray. E Zoomed-in image of the box plot in D showing an overlay of cell masks on Vcam1 antibody and DAPI signal. The cell masks are colored according to the ME assignment of each cell. The Vcam1 signal is shown in white over the DAPI gray signal. F Expression of top injury marker genes in injured PT cells within ME-5 and the Injured PT cells outside ME-5 in Control samples (left) and AKI (right). (*p < 0.05; **p < 0.01 of a paired two-sided t test). Source data are provided as a Source Data file. G Normalized expression of injury markers in Injured PT cells within ME-5, sorted by the eccentricity of each cell. Cells were sorted according to eccentricity values, and the gene expression was averaged using a moving window with a window size of 10% total number of cells. Expression values were normalized for each gene in the heatmap.