Extended Data Fig. 4: Characterization of spermatogenesis/spermatogonia in Stag3 KO mice.
From: The mitotic STAG3–cohesin complex shapes male germline nucleome
a, UMAP and Louvain clustering of scRNA-seq data of WT and Stag3 KO mouse testes at P15. Cells were classified into 12 distinct populations, as indicated. UndiffSg: undifferentiated spermatogonia; DiffSg: differentiating spermatogonia. b, Expression of spermatogonia markers and a Sertoli marker (Sox9) in the UMAP in (a). c, Distribution of WT and Stag3 KO cells in the UMAP in (a). d, UMAP and Louvain clustering of the spermatogonia population (cluster1) in (a). The spermatogonia were classified into “stem-cell” (cluster 1), “intermediate” (cluster 2), “differentiation-primed” (cluster 0), and “differentiating” (cluster 3) spermatogonia. e, Marker gene expression in the four populations described in (d). f, Violin and box plots of the normalized expression of the indicated genes in WT and Stag3 KO spermatogonia at P15. Box plots are as in Fig. 2d. p-values are measured by two-sided Welch’s t-test. Each box plot includes 2,616 WT and 2,418 KO cells. p-values shown in the panels are as follows: Id4 (6.3 × 10−5), Dusp6 (3.2 × 10−3), Neurog3 (1.6 × 10−3), Gfra1 (1.3 × 10−2), Sox3 (6.9 × 10−3), Rarg (2.9 × 10−3). g, UMAP and Louvain clustering of scRNA-seq data of WT and Stag3 KO undifferentiated spermatogonia at 8 weeks. Cells were classified into 11 distinct populations, as indicated. StemCellSg: “stem-cell” spermatogonia; Diff.Primed: “differentiation-primed” spermatogonia; EarlyMs: early meiotic cells; LateGerm: late-stage germ cells, including spermatocytes and spermatids. h, Spermatogonia marker expression in the UMAP in (g). i, Violin and dot plots of the normalized expression of the indicated genes in the clusters for undifferentiated spermatogonia [clusters 0 − 6 in the UMAP in (g)]. j, Correlation of Stag1, Stag2, and Stag3 with genes in undifferentiated spermatogonia [cluster 0 − 6 in (g)] in 8-week testes. The genes on the X-axis are ordered by correlation. k, Immunofluorescence (IF) analysis for GFRA1 (magenta), SOX9 (cyan), and PLZF (yellow) expression in P15 WT and Stag3 KO testes. Bar, 50 μm. For each genotype, a total of four slides were analyzed, prepared from two testes obtained from two different mice (two slides per testis).
