Fig. 3

Isl1 orchestrates a complex gene regulatory network driving cardiogenesis. a, b Heatmap representation of RNA-Seq analysis of dissected pharyngeal mesoderm and hearts of wild-type and E8.75 Isl1 knockout embryos (a) as well as dissected OFT and RV of E10.5 wild-type and Isl1 hypomorphic embryos (n = 4, fold change >1.5; log2 fold change <−0.58, >0.58; p-value < 0.05) (b). GO terms enriched among genes downregulated or upregulated upon Isl1 loss-of-function and representative genes within these GO terms are presented on the right side of the panel. c Venn diagram representing the overlap of genes bound by Isl1 in E8.25-E9 embryos or ESC-derived CPCs (n = 2) and differentially expressed in dissected pharyngeal mesoderm/ hearts of E8.75 Isl1 knockout embryos as well as OFT and RV of E10.5 Isl1 hypomorphic embryos compared to control embryos (n = 4). d Isl1-regulated gene network identified using GeneMANIA and Cytoscape. e–g GO terms enriched in genes bound by Isl1 in ESC-derived CPCs or E8.25-E9 embryos and deregulated in E8.75 Isl1 knockout embryos (e), in E10.5 OFT+RV of Isl1 hypomorphic embryos (f), or in both E8.75 Isl1 knockout embryos and E10.5 OFT+RV of Isl1 hypomorphic embryos (g). Examples of genes regulated and bound by Isl1 in (e–g), showing genome tracks of Isl1 ChIP-Seq in CPCs and RNA-Seq reads, are presented on the right side of the panel