Fig. 2

Identification of Nanog-responsive genes. a ChIP analysis of Nanog binding across a set of targets, as indicated on the X-axis. Each dot represents measurements in individual replicates (n = 4; 2 for each independent SunTag clone). b Normalised levels of Esrrb (top) and Klf4 (bottom) mRNA after the indicated number of days in the absence/presence of Dox. Each dot represents measurements in individual replicates as in a. c MA Plots displaying log2 fold changes as indicated on the Y-axis as a function of average expression. RNA-seq was performed in both SunTag (72 h Dox induction) and 44iN cells (24 h Dox withdrawal). Red and blue represent differentially expressed genes (FDR < 0.05). d Boxplot of the log2 fold change for the genes identified in c as upregulated (red) or downregulated (blue) by Nanog, in either SunTag (left) or 44iN cells (right), measured in both inducible systems as indicated on the X-axis. For each boxplot, the central line represents the median, the limits the lower/upper quartiles, and the whiskers the most extreme data-point within 1.5 times the interquartile range in excess of the lower and upper quartile. e Heat map representing gene expression z-scores of all transcripts identified by combining SunTag (FDR < 0.05), 44iN (FDR < 0.05) and SunTag/44iN likelihood ratio test (FDR < 0.05) datasets