Figure 2
Whole-genome expression analysis of wild-type and Zfp57-/- hybrid day-12 cells. (a,b) Cluster analysis of RNAseq data focusing on all genes (a) or imprinted genes (b) of day 0 and day 12-wild-type and Zfp57-/- JB1 cells. Zfp57-/- cells are indicated by a red line. (c) Heatmap representing lineage-specific marker expression in wild-type and Zfp57-/- JB1 cells derived from RNAseq analysis. The public datasets (references indicated) were retrieved from the GEO database (Supplementary Table 1). The new datasets are indicated with bold characters. The heatmap was created using R package "pheatmap version 1.0.12" (https://CRAN.R-project.org/package=pheatmap). (d) Scatter plot showing deregulated genes in Zfp57−/− day 12-JB1 versus wild-type day 12-JB1 cells. Deregulated genes are indicated by red dots if downregulated (non-imprinted genes by light-red; imprinted genes by dark-red) and by blue dots if upregulated (non-imprinted genes by light-blue; imprinted genes by dark-blue). (e) Cumulative distribution of the distances (bp) of deregulated genes (imprinted genes: green; non-imprinted genes: orange) in Zfp57-/- day 12-JB1 cells from the ZFP57 target sites determined in wild-type day 0-JB1 cells24. The difference between the two curves is statistically significant according to the two-sample Kolmogorov–Smirnov test (p-value < 1e-10). (f,g) Gene ontology analysis of differentially expressed genes in Zfp57−/− day 12-JB1 cells (f, upregulated; g, downregulated). Bars represent GO:BP terms sorted by high to low -log10 (adjusted p-value). (h) Gene ontology analysis of down-regulated genes located < 100 Kb from ZFP57-KAP1 binding sites.
