Figure EV3. 5C state is a new pluripotency state (related to Fig 5).

• A
  Summary of characteristics of PSCs in 5C state, formative state, and EpiLCs state.
• B, C
  Top 1,000 upregulated genes (compared to ESCs) were selected from the current RNA‐Seq and previously reported datasets (Data ref: Hayashi et al, 2011; Data ref: Bertone, 2014) for the three states. The overlapping was determined (B). In addition, the genes which were upregulated in primed PSCs (compared to ESCs, based on the current RNA‐Seq) were further selected and listed in (C).
• D, E
  Two different datasets were used to repeat the studies in (B and C) (Data ref: Buecker, 2014; Data ref: Kalkan et al, 2019).
• F
  The genes which were only upregulated in one of the three states were used for GO analysis.
• G, H
  Single‐cell qPCR was performed with 5C‐Oct4GFP⁺ cells (120 cells), R1 ESCs (48 cells), and R1 ESCs‐primed (cells). Dppa3, Esrrb, Fbxo15, Klf2/4/5, Nanog, Prdm14, Tbx3, Tfcp2l1, and Zfp42 were used as naive markers, while Cer1, Fgf5, Foxa2, Lef1, Nodal, Sox1, and T were used as primed markers. The average expression of naïve and primed markers was calculated for each cell and was used to plot the cells in (G). Heatmap summarized results (H, left), and the average expression of each gene in 5C‐Oct4GFP⁺ cells (5C), R1 ESCs (naïve), and R1 ESCs‐primed (primed) was provided and compared (H, right).

Data information: Statistical information is listed in Dataset EV7.