A rich stem cell–regulatory genetic network controlled by a composite cis-element. RNA-seq-based comparison of gene expression in E11.5 +9.5^+/+ (n = 3) and +9.5^−/− (n = 3) cultured AGM explants. (A) MA plot for +9.5^−/− versus +9.5^+/+ cultured AGM explants. The red points indicate 778 and 182 genes down- or up-regulated (FDR < 0.05), respectively, in the mutants. (B) Heatmap depicting statistically significant, differentially expressed genes down- or up-regulated by >16 fold. (C) Gene Ontology analysis of genes down- or up-regulated in +9.5^−/− cultured AGM explants with a cut-off FDR <0.05 using DAVID Bioinformatics Program (http://david.abcc.ncifcrf.gov/). The most enriched biological processes are shown with corresponding P values. (D) RNA-seq-based analysis of the expression levels of representative genes expressed in HSCs and the HSC niche that regulate hematopoiesis, as well as genes expressed in endothelium, erythroid, myeloid, and lymphoid cells (*, FDR < 0.05). (E) The relative expression levels (TPM, transcripts per million) of representative genes shown in the figure.