Extended Data Fig. 4: Transcriptome network in in vitro induced PGCLCs.

(A and B) Venn diagram for significantly upregulated (Log2 (FC) > 1 and FDR < 0.05) (a) and downregulated (Log2 (FC) <-1 and FDR < 0.05) (b) DEGs in N3⁺PGCLC, DM⁺PGCLC and DZ⁺PGCLC d8 versus 4i ES cells. The number of genes for each category is indicated in the Venn diagram. Text boxes show representative PGC genes and related Gene Ontology (GO) biological processes terms significantly enriched with FDR values. The data represents an integration of two biological replicates. FC: Fold Changes. (c) Immunofluorescence for marker genes in 4i ES cells, N3⁺PGCLC, DM⁺PGCLC and DZ⁺PGCLC (day 4 (d4), day 8 (d8), no DEX/dox control for 8 days (Neg)). TFCP2L1 for 4i ES cells shows high background signal. Scale bar: 100 μm. The experiment was repeated independently two times with similar results. (d) Gene set enrichment analysis (GSEA) for DM⁺PGCLC and DZ⁺PGCLC d8 versus 4i ES cells based on RNA-seq against marker genes for migratory, mitotic, and mitotic arrest PGCs. E-score (enrichment score) and nominal p-value are indicated. The p-values for the GSEA test statistics are calculated by permutation. The data represents an integration of two biological replicates. (e) UMAPs of 4i ES cells, N3⁺PGCLC, DM⁺PGCLC and DZ⁺PGCLC d8 scRNA-seq dataset (each from single biological sampling points) batch-corrected with Harmony. Expression of DDX4 and PIWIL4 shown in log transformed (normalized count (NC) + 1).