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. 2025 Nov 10;26(6):bbaf586. doi: 10.1093/bib/bbaf586

Figure 6.

UMAP and dot plots displaying the mouse testis reference atlas and projections of wild-type and knockout germ cells, highlighting differences in cell-type composition and developmental pseudotime trajectories.

Mapping the genetically perturbed germ cells to mouse testicular cell atlas (mTCA). We built a reference of wild-type (WT) mouse testicular cells from 6.5 days post coitum (dpc) to adults and then mapped two datasets consisting of paired samples from WT and knock-out (KO) mice. (a) UMAP of WT mouse testis reference (n = 188,862 cells), colored by major cell types (upper right), age (lower right), and cell subtypes (left). Each dot represents a single cell. (b) Dot plot for expression of representative signature genes of testicular cells. The dot size represents the percentage of cells expressing the indicated genes in each stage and the dot color represents the average expression level of the genes. (c) Projection of WT and Zfp541-KO germ cells onto the testis reference. Grey dots represent reference cells, query cells colored by cell types predicted via ProjectSVR using a 10-NN classifier on reference embeddings. D. The cumulative distribution of cells along pseudotime from each mouse strain. The pseudotime was predicted via ProjectSVR from mTCA. (e, f) The same plots as in (c, d) were applied to Ythdc2-KO germ cells.