Fig. 4

Transcriptional analysis of IL-11 + VEGF and IL-11 + sIL-11Rα + VEGF. (A) Experimental setup for RNA Seq analysis from 3D cell culture setting. N = 3 independent experiments using HUVECs with 14-22 spheroids per group and experiment. (B) PCA analysis of all samples. (C) Total number of up- and downregulated DEGs compared to VEGF (control). (D) Scatter blot visualizing all genes with at least one count when comparing IL-11 + sIL-11Rα + VEGF against IL-11 + VEGF. Differentially expressed genes (DEGs) were defined by padj <0.05 and abs(log2 foldchange) >1. The five most expressed up- and downregulated DEGs are labeled. All following analyzes were conducted by comparing IL-11 + sIL-11Rα + VEGF against IL-11 + VEGF. (E) The five most significantly enriched and depleted biological processes according to Gene Ontology (GO) terms. Positive normalized enrichment score (NES) refers to enrichment in the IL-11 + sIL-11Rα + VEGF treatment and negative NES to depletion and consequently enrichment in IL-11+VEGF. (F) Gene Set Enrichment Analysis (GSEA) for the GO term “angiogenesis” (GO:0048514). (G) Heatmap illustrating the 20 leading edge genes of the GSEA from F