Figure 4
Expression profiling of LIF-independent iOCT4 ES cells (A) K-means clustering analysis of RNA-Seq data. Differentially expressed genes (> two-fold) clustered according to k-means. (B) Scatter plot of RNA-Seq gene expression analysis between two LIF-independent iOCT4 ES cell clones (#4 and #5) (top left), and between LIF-independent iOCT4 ES cells and control ES cells (bottom left), EpiSCs (top right), MEFs (top middle), or day 14 embryoid body (EB) differentiated ES cells (bottom right). Log2 adjusted differentially expressed genes are plotted (> two-fold, RPKM >1, FDR <0.001). (C) Principal component analysis (PCA) of differentially expressed genes between LIF-independent iOCT4 ES cells, control ES cells, EB-differentiated cells, EpiSCs, and MEFs. (D) Custom tracks of RNA-Seq data in the UCSC genome browser. (E) GSEA analysis of STAT3 targets between control ES cells and LIF-independent iOCT4 ES cells. (F) Correlation matrix of differentially expressed (DE) genes between control ES cells and LIF-independent iOCT4 ES cells with promoter binding of transcription factors and epigenetic modifiers. Heat map generated by evaluating pair-wise affinities between DE genes using RNA-Seq datasets generated from this study and published ChIP-Seq data9,23,24,25. AutoSOME73 was used to generate pair-wise affinity values.
