Figure 2.

Genes Differentially Expressed in P53^−/− ESCs

(A) Principal component analysis on gene expression of WT and P53^−/− G1-phase ESCs cultured in serum and 2i conditions.

(B) Volcano plot showing the transcriptome changes in 2i or serum P53^−/− G1-phase ESCs compared with WT. Each dot represents one gene. Significantly changed genes (adjusted p value <0.1 and a fold change of 1.5) are colored (downregulated genes in green/blue and upregulated genes in red/purple).

(C) Venn diagram showing the overlap of DE genes in serum and 2i.

(D) Fraction distribution showing the fraction of genes differentially expressed between WT and P53^−/− ESCs cultured in either serum or 2i.

(E) GO analysis revealing the significant biological processes in serum or 2i ESCs. Number of genes present for each category are indicated at the right. For the RNA-seq analysis, we made use of P53^−/− FUCCI (clones 1 and 2).

(F) Serum WT and P53^−/− FUCCI (clone 1) ESCs treated with or without doxorubicin (1μM, 16 h), stained by PI and analyzed on fluorescence-activated cell sorting to assess apoptosis. Experiment performed in triplicate, numbers indicate mean percentage apoptotic ESCs (sub-G1 phase) plus SD. At least two independent experiments showed similar results.