Fig. 1: Lineage-specific up-regulation of LTR5Hs in hPGCLC induction.

A Schematic illustration of hPGCLC in vitro differentiation procedure. B Heatmap for the top 200 TE subfamilies with the highest cross-sample variation in hESCs, iMeLCs, and hPGCLCs. The colored bar on the left indicates TE class. C Pie chart showing the proportion of up- or down-regulated DETE copies in hPGCLCs compared to hESCs using a cut-off of at least a 4-fold change and FDR <0.05. D Top 10 up- or down-regulated TE subfamilies in hPGCLCs. X axis shows DETE copy numbers proportional to the total copy number of a specific TE subfamily. Only TE subfamilies with at least 80 copies and 8 DETE copies are kept for this analysis. E Screenshots showing representative hESC and hPGCLC RNA-seq tracks over LTR5Hs integrants. Red shaded rectangle region indicates individual LTR5Hs copies. F Scatterplot for aggregated expression level of each TE subfamily in hESCs and hPGCLCs. The size of each dot represents the proportion of DETE copy numbers relative to the total copy number of each TE subfamily. G Scatterplot of the expression of individual TE copies belonging to the top three up- or down-regulated DETE subfamilies. Gray dots represent TE copies which are not differentially expressed. H UMAP of scRNA-seq dataset for two replicates (r) of UCLA2 hESCs, iMeLCs, and D1 to D4 hPGCLCs (left), representative expression pattern for NANOS3, LTR5Hs, and HERVK. Differentiation trajectory of hPGCLCs is denoted by arrows, hPGCLC population is indicated by dashed line. DETE analysis for this figure is analyzed by the STAR + featureCounts+DESeq2 method. Source data underlying B, D, and F are provided as a Source Data file.