Cell-type-specific binding of SOX2 in CNS and endoderm progenitors.

<p>(<b>A</b>) E11.5 <i>Sox2-Gfp</i> knock-in embryo shows expression in the cortex and spinal cord, while inset highlights expression in dissected stomach and lung/esophagus. (<b>B</b>) Overlapping expression of SOX2 and Ki67 in cycling progenitors of the E11.5 cortex, spinal cord, stomach and lung. Grey areas in diagrams represent SOX2⁺ stem cells, while tan surroundings in stomach and lung represent non-endodermal derived mesenchymal cells. (<b>C</b>) Central enrichment of SOX2 binding motifs in cortex, spinal cord, stomach and lung/esophagus SOX2 ChIP-seq peaks. The percentage of peaks that the given motifs are found centrally enriched, and their p-values are listed. (<b>D</b>) Venn diagram showing overlap between sites bound in the different SOX2 ChIP-seq experiments. 32 peaks overlapped in all four tissues. (<b>E</b>) Representative tracks showing germ-layer-specific and common SOX2 ChIP-seq reads aligned around <i>Foxa2</i>, <i>Neurog2</i> and <i>Axin2</i> gene loci, with magnification of selected peak sites. Tracks from cortex are in red, spinal cord in green, stomach in blue and lung/esophagus in yellow, with read scale maximum labelled on y-axis. Inset black lines are centred on peaks. (<b>F</b>) Toppcluster Fruchterman-Reingold Network of the top ten GO terms enriched for genes bound by SOX2 in the cortex, spinal cord, stomach and lung/esophagus. (<b>G</b>) Diffbind PCA of SOX2 ChIP-seq duplicates in cortex, spinal cord, stomach and lung/esophagus, as well as published SOX2 ChIP-seqs in ESCs, ESC derived NPCs and adult stomach.