Extended Data Fig. 10: Common features of scRNA-seq and bulk RNA-seq datasets.

a, Terms significantly enriched among genes downregulated in BG(95%) (loser) ESCs in vitro when co-cultured with HB(24%) cells. The loss of mitochondrial activity emerges as a common feature between loser cells in vivo and in vitro. The gene enrichment analysis was performed using g-profiler tool (see Methods) and p-values were adjusted for multiple comparisons using the g:Profiler algorithm g:SCS (10.1093/nar/gkm226). b, Intersection between differentially expressed genes along the trajectory from winning to losing epiblast cells (‘in_vivo_scRNA-seq’; Fig. 2a and Extended Data Fig. 3a, and genes differentially expressed between co-cultured HB(24%) (winner) and BG(95%) (loser) ESCs (‘in_vitro_bulk_RNA-seq’). ‘Up’ and ‘Down’ here refer to genes up- or down-regulated in loser cells. For the intersection between down-regulated genes from scRNA-seq (in vivo) and down-regulated genes from bulk RNA-seq (in vitro): p-value, 1.71E-12; odds ratio 1.80. For the intersection between down-regulated genes from scRNA-seq (in vivo) and up-regulated genes from bulk RNA-seq (in vitro): p-value, 5.20E-3; odds ratio 0.67. For the intersection between up-regulated genes from scRNA-seq (in vivo) and down-regulated genes from bulk RNA-seq (in vitro): p-value, 4.87E-3; odds ratio 0.80. The intersection between up-regulated genes from sc-RNA-seq (in vivo) and up-regulated genes from bulk RNA-Seq (in vitro) is not statistically significant: p-value: 0.30, odds ratio 1.14. c, Intersection between the significantly enriched terms in genes upregulated or downregulated in loser cells in the epiblast of CI-treated embryos (‘in_vivo_scRNA-Seq’) or in our in vitro model of competition between co-cultured HB(24%) (winner) and BG(95%) (loser) ESCs (‘in_vitro_bulk_RNA-seq’). All the terms enriched among downregulated genes in vitro are also enriched in vivo. See methods for details on statistical analysis.