Fig. 1

Global assessment of the transcriptome during mesendoderm specification. a Pie chart showing composition of the Poly (A)⁺ transcriptome, Protein Coding Genes (PCG, blue), Ensembl lncRNAs (yellow) and non-annotated lncRNAs (red). b Kernel density plot of coding potential (Gene ID score) of PCGs, Ensembl lncRNAs and non-annotated lncRNAs. c Box plot whiskers of transcript abundance (FPKM) of PCGs (blue), Ensembl lncRNAs (yellow) and non-annotated lncRNAs (red). p values were calculated using a two-tailed t test. (****P < 0.0001). d Expression heatmap of representative PCGs in ESC, Eo ⁻ and Eo ⁺. Markers of pluripotency, Primitive Streak/Mesendoderm (PS/ME), cardiac mesoderm and early ectoderm/neuroectoderm are shown. e Hierarchical clustering of Ensembl lncRNA expression across ESC, Eo ⁻ and Eo ⁺. Enriched GO terms and example PCGs are shown to the right. f Hierarchical clustering of non-annotated lncRNA expression across ESC, Eo ⁻, and Eo ⁺. Enriched GO terms and example PCGs are shown to the right. g Kernel density plot of the specificity of PCG and lncRNA assessed by quantifying the normalized difference of expression in the three conditions (ESC, Eo ⁻ , Eo ⁺). h Co-activation of selected PCGs and divergent lncRNAs involved in ME specification. i RNAseq reads in ESC, Eo ⁻ and Eo ⁺ at the Lhx1 locus. A divergent lncRNA (Lhx1os) is shown