Figure 3

Transcriptional landscape of whole kidney marrow cells of IT325 mutants. (a) Uniform manifold approximation and projection (UMAP) representation of transcriptome similarities determined by combined analysis of 341 wild-type and 331 mutant cells of the IT325 line; the individual clusters are indicated by colour and numbers. (b) Distribution of wild-type and mutant cells among transcriptionally defined cell clusters; genotypes of cells are colour-coded. (c) Expression pattern of signature genes (listed at the bottom) in the individual cell clusters shown in (a, b). Colour represents the z-score of the mean expression of the gene in the respective cluster and dot size represents the fraction of cells in the cluster expressing the gene. z-scores above 1 and below -1 are replaced by 1 and −1, respectively. (d) Cell type identification based on signature gene expression patterns (see Table 2, and text for details). (e) Graph representation of neighbourhoods identified by the Milo algorithm; the positions of index cells of neighbourhoods are projected onto their positions of the UMAP representation shown in (a, b). Nodes are equivalent to neighbourhoods; colours indicate their compositional differences between wildtype and mutant cells and are quantified as log₂ fold changes at FDR 10% (colour code is indicated to the right); the sizes of the nodes denote the number of cells in the neighbourhood; graph edges represent the number of cells shared among adjacent neighbourhoods. (f) The distribution of log₂ fold changes in abundance between wildtype and mutant cells in neighbourhoods identified in different cell clusters (identified at the left) is shown in a bee-swarm plot; neighbourhoods exhibiting differential abundance at FDR 10% are colour-coded (reddish colours denote greater abundance of mutant cells; bluish colours denote greater abundance of wildtype cells).