Figure 5.
Transcriptome Analysis of Single and Combined Mutants
(A and B) Hierarchical clustering (A) and PCA plot (B) based on normalized gene expression for all genes. ∗ denotes cells expanded in CH/LIF and switched to 2i for 48 h prior to sample conditions.
(C and D) Heatmaps showing relative expression for pluripotency genes (C) and lineage markers (D). Values are shown as Log2 fold change of RNA-seq read counts relative to RGd2 2i-p5. Only the genes with a mean expression value of FPKM ≥ 1 in either RGd2 2i-p5 or ETR-tKO N-p5 samples were included. Genes were sorted by mean expression within each group.
(E) KEGG pathway enrichment for differentially expressed genes.
(F) MA plot showing mean expression against fold change per gene in ETR-KO cells cultured in N2B27 for 5 passages (ETR-tKO N-p5) versus RGd2 2i-p5 sample. Gene symbols are shown for selected genes listed below.