Fig. 4.

Transcription profile of SCC knockdown mESCs. (A) Comparative expression of pluripotency (Left) and differentiation (Right) markers between SCC KD and WT mESCs, evaluated by RNA-seq. Genes whose expression is not changed (NC) are listed in boxes. Plotted is the log₂ ratio of SCC KD and WT RPKM counts (details on SCC KD generation in Fig. S4; global pairwise comparisons of RPKM values in Fig. S5A; qPCR validation of selected genes in Fig. S5B; full gene list in Dataset S2). (B) Protein levels of selected genes in SCC KD vs. WT mESCs, β-actin normalized. Plotted are average signal and SD of two independent Western blots quantified by ImageJ (representative blot in Fig. S5C). P-STAT3, antibody detecting active, Tyr705-phosphorylated STAT3. Analysis of p-53 targets in Fig. S5G. (C) Clonal assays in SCC KD compared with WT mESCs. Plotted is the number of AP⁺ colonies obtained from plating 300 cells in six-well plates (average and SD of three independent experiments). (D) GO analysis of genes up-regulated (UP) and down-regulated (DOWN) in SCC KD mESCs compared with all annotated genes. Bracketed is the number of deregulated genes belonging to each category. EASE (Expression Analysis Systematic Explorer) scores < 0.01 for all categories (complete table in Dataset S2). (E) Percentage of genes bound by RAD23B and OCT4/SOX2 within 5 kb from their TSS among genes either not changed (NC), down-regulated (DOWN), or up-regulated (UP) upon SCC KD. The number of genes in each category is specified (n). ***P < 10⁻³, two-sample test for equality of proportions with continuity correction. Data of SCC KD mESCs are average of two independent Xpc shRNA constructs in Rad23b^−/− mESCs.