Supplementary Figure 4: Analysis and comparison of Prdm15Δ/Δ and Prdm14–/– ESC transcriptomes.
From: PRDM15 safeguards naive pluripotency by transcriptionally regulating WNT and MAPK–ERK signaling
(a) Scatterplot of RNA-seq expression analysis in Prdm15fl/fl versus Prdm15Δ/Δ ESCs cultured either in SL (top) or 2i (bottom). The numbers of upregulated (red) and downregulated (blue) genes are indicated on the graphs. Highlighted are Spry1 and Rspo1 (which are downregulated upon PRDM15 depletion in both conditions) and Wif1 whose expression is upregulated in Prdm15Δ/Δ ESCs under SL conditions but rescued by 2i. (b) Venn diagram depicting the overlap among differentially expressed genes in Prdm15-knockout versus Prdm14-knockout (top) and Prdm15-knockout versus Mtgr1-knockout (bottom) ESCs in SL and 2i conditions. (c) Differentially expressed genes between Prdm15fl/fl and Prdm15Δ/Δ ESCs in 2i versus SL conditions, identified by RNA-seq (3 d after deletion (n = 3)). Four main clusters have been identified. Cluster 1 and clusters 2/3 comprise genes up- and downregulated, respectively in Prdm15Δ/Δ cells, yet rescued by 2i. Cluster 4 contains genes unaffected by PRDM15 deletion in both conditions (2i and SL). The most dominant categories enriched in each cluster are indicated.
