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. 2023 Aug 23;12:RP85380. doi: 10.7554/eLife.85380

Figure 6. Single-cell RNA-sequencing (scRNA-seq) analysis of THY1+ undifferentiated spermatogonia (uSPG) in Foxc2f/+ and Foxc2f/-;Ddx4Cre/+ mice.

(A) Schematic illustration of the scRNA-seq workflow. (B) t-SNE plot and developmental trajectory of uSPG from Foxc2f/+ and Foxc2f/-;Ddx4Cre/+ mice, respectively, colored by cluster. (C) Developmental trajectories of uSPG from Foxc2f/+ and Foxc2f/-;Ddx4Cre/+ mice, colored by sample or derivation. (D) Developmental trajectories of the cells in Cluster1 from Foxc2f/+ (CON) and Foxc2f/-;Ddx4Cre/+ (KO) mice, colored by derivation or developmental state. (E) The Cluster1 cells proportion of each state in CON and KO mice. (F) Heatmap showing the differentially expressed genes (DEGs) in the Cluster1 cells from the Foxc2f/-;Ddx4Cre/+ mice compared with the Foxc2f/+ mice. (G) Top Gene Ontology (GO) terms enrichment by the down-regulated DEGs in KO mice. (H) Gene set enrichment analysis (GSEA) of the Cluster1 cells (Foxc2f/-;Ddx4Cre/+ v.s. Foxc2f/+ mice). NOM, nominal; FDR, false discovery rate; ES, enrichment score; NES, normalized enrichment score.

Figure 6—source data 1. Excel spreadsheet with the list of the differentially expressed genes found by single-cell RNA-sequencing (scRNA-seq) and enriched Gene Ontology terms.

Figure 6.

Figure 6—figure supplement 1. Single-cell RNA-sequencing (scRNA-seq) analysis of THY1+ undifferentiated spermatogonia (uSPG) in adult Foxc2f/+ and Foxc2f/-;Ddx4Cre/+ mice.

Figure 6—figure supplement 1.

(A) Feature plots of classic SPG markers for uSPG in adult Foxc2f/+ or Foxc2f/-;Ddx4Cre/+ mice. (B) Expression dynamics of SPG markers with pseudotime progression for uSPG from Foxc2f/+ or Foxc2f/-;Ddx4Cre/+ mice, respectively. (C) Expression dynamics of SPG markers with pseudotime progression for overall uSPG from Foxc2f/+ and Foxc2f/-;Ddx4Cre/+ mice.
Figure 6—figure supplement 2. Re-cluster and developmental trajectory analysis of cells in Cluster1 derived from adult Foxc2f/+ and Foxc2f/-;Ddx4Cre/+ mice.

Figure 6—figure supplement 2.

(A) The t-SNE plot of the Cluster1 cells aggregated from the Foxc2f/+ and Foxc2f/-;Ddx4Cre/+ mice colored by sample or subcluster. (B) The cell proportion of each sample in each subcluster. (C) Feature plots of SPG markers expression. (D) Developmental trajectory of the aggregated Cluster1 cells colored by subcluster or pseudotime. (E) Expression dynamics of SPG markers with pseudotime progression.