Fig. 4: Isolating elite human PS cells having high naïve induction potential.

a, Overview of the experiment to identify elite human PS cells having high naïve induction potential. b, Clonal abundance distributions of barcoded clones in tier 1 (T1) and tier 2 (T2) primed and native stem cells before and after naïve induction. An average value of two replicates (n = 2) is reported for each barcoded clone. n.d., not determined. c, Correlation in barcoded clone abundance between T1 and T2 naïve cell samples. d, Isolation of elite human PS cell clone candidates having high naïve potential from the parental population. The CloneSelect C→T reporter was activated by electroporating Target-AID and gRNA plasmids. The sorted clones were expanded and subjected to naïve induction followed by trophoblast differentiation. e, Isolated elite human PS cell clones (n = 1). Scale bar, 100 µm. f, Microscopic images and flow cytometric profiles (n = 2) of the isolated elite human PS cell clones. Scale bar, 100 µm. CD24 and SUSD2 boundaries to call primed and naïve cells are represented by the red lines, and median marker intensities are shown by bold black lines. g, Microscopic images and flow cytometric profiles (n = 2) of the isolated clones after naïve induction. %+ve, percent positive. h, Differentially expressed genes in the primed state between the parental cells and isolated clones (n = 2). i, Transcriptome and DNA methylation track at a chromosome X locus for the parental cells and isolated elite clones in the primed state (n = 2). j, Differentially expressed genes in the naïve state between the parental cells and isolated clone cells. k, Gene set enrichment analysis for the elite clone-specific downregulated genes after naïve induction. Gene Ontology terms were clustered by spring-embedding a network representation of the Gene Ontology term hierarchy relationships using Cytoscape. FDR, false discovery rate.