Fig. 4

CROP-seq on mouse embryonic stem cells (mESC) uncovered known regulators for stem cell differentiation. a The t-SNE plot on single-cell expression profiles in naïve or primed states in two batches. b Selected marker expression, including Esrrb, Nanog (naïve markers), Otx2, and Dnmt3b (primed markers). c The adjusted p values, calculated from scMAGeCK-RRA, on target gene downregulation. d The naïve marker scores as well as primed marker scores in their corresponding cell states. Genes with FDR < 0.05 are highlighted in red. Naïve marker score is based on the average expression of four naïve marker genes: Nanog, Esrrb, Klf4, and Tdh, while primed marker score is based on Otx2 expression. e The target-marker-phenotype network constructed from scMAGeCK results. Only significant results (FDR < 0.01) are used to construct the network. Dotted arrow indicates Esrrb-Otx2 that is inconsistent with known Esrrb functions