Effect of 3-D culture on the expression of naïve pluripotent markers in primed ESCs. (A) Expression of select core (OCT4, NANOG, and SOX2), primed (FOXA2, ZIC2, SALL2, and SOX11), and naïve (KLF2, ESRRB, DNMT3L, KLF17, STAT3, DPPA3, TBX3, PRDM14, KLF5, ZFP42, TFCP2L1, FGF4, and GDF3) pluripotent markers in ESCs cultured in 3-D scaffolds for 21 days and 2-D grown primed ESCs (H9 cells) and naïve ESCs (Elf1 cells, set to control) was analyzed by qRT-PCR. Results were expressed as the fold expression ± SE normalized to reference genes HMBS, GAPDH, and β-ACTIN (* p < 0.05 and ** p < 0.01).