Fig. 1

Spatial cell-type annotation in the human embryonic kidney from 18 weeks post-conception. a A schematic diagram displaying the artificial division of the three compartments (cortex, medulla, and pelvis regions) of the kidney based on histomorphology. t-SNE shows the cell types identified with all the single cells, and colors indicate the 15 spatial clustering assignments; b Multimodal intersection analysis (MIA). The hypergeometric test was applied to evaluate the significant intersection of the respective genes specifically identified in a given cell type (podocyte in this case) and region-specific gene sets (see “Materials and methods” section). c MIA map of all scRNA-seq-identified cell types and ST-defined clusters. Each element in the matrix was computed as described in (b) for all pairs of cell types and tissue regions using the same 27,008 background genes. The bar on the bottom indicates – log10 (P-value) calculated by hypergeometric test. *Represents the closest relationship between scRNA-identified cell types and the ST-defined clusters (P < 0.01). d Space projection of scRNA-identified cell types on the kidney tissue from 18 weeks post-conception. Scale bar: the blue to red gradient corresponds to the matching degree between cell-type-specific (scRNA-seq) and region-specific (ST-seq) gene sets. PCW, post-conception weeks; ICs, interstitial cells; PTA, pretubular aggregate; UBCD, ureteric bud/collecting duct; SSBmd/DTLH, distal tubule/loop of Henle and s-shaped body medial precursor cell; NPC, nephron progenitor cell; SSBpr, s-shaped body proximal precursor cell; ErprT, early proximal tubule. PETE, Pelvic segment transitional epithelium; Mes, mesangial cell; Pod, podocyte