Extended Data Fig. 2: Expression of endothelial transcripts in the FLK1⁺ cell population at day 7 post-ETV2 induction during MEF reprogramming.

(a) The violin plots show the scaled expression levels of endothelial markers such as Etv2, Emcn, Lmo2, Flk1/Kdr, Cdh5 and Sox18 in MEFs, day 1, day 2, day 7 post-ETV2 induction, as well as the FLK1⁺ cells from day 7. The y-axis indicates the gene expression levels scaled and normalized by Seurat. (b) The violin plots show the scaled expression levels of endothelial markers in seven cell clusters. The y-axis indicates the gene expression levels scaled and normalized by Seurat. The one-sided enrichment test was used to evaluate the significance of pathway enrichment. The p-value adjustment was performed by B-H Procedure. (c) The biological processes that are significantly associated with the up-regulated in genes in cluster 1 (undifferentiated MEFs) compared with the rest of the cell populations. There are 3,562, 948, 2,936, 7,202 and 827 single cells from undifferentiated MEFs, MEFs with day 1, day 2, day 7 post-ETV2 induction, and FLK1⁺ cell population of day 7 post-ETV2 induction, respectively. (d) GSEA plot indicates significant upregulation of the inflammatory response in MEFs (cluster 1). The y-axis representing the enrichment score (ES) for each gene and x-axis indicates the gene rank in the ordered list. The default GSEA permutation test was used to evaluate the significance of gene set enrichment. No p-value adjustment was performed. (e) Heatmap representing the gene expression levels scaled by Seurat for upregulated (red) and downregulated (blue) genes in cluster 1 and cluster 2. (f-g) The bar plots show top 10 significant pathways for cluster 1 and cluster 2 for MEFs. The y-axis represents the p adjusted values obtained from over-representation test in Gene Ontology enrichment analysis. The one-sided enrichment test was used to evaluate the significance of Gene Ontology enrichment. The p-value adjustment was performed by B-H Procedure.