Recent evolution of the developing human intestine impacts metabolic and barrier functions
Description
This is the additional supporting data for the manuscript titled as "Recent evolution of the developing human intestine impacts metabolic and barrier functions". It contains 1) comprehensive annotation of open chromatin regions detected in developing human or chimp intestine organoids or tissue; 2) cell type enriched features, including (A) developing human proximal small intestine tissue cell type marker genes and regions, (B) in vitro and transplanted HIO cell type enriched genes and regions, (C) in vitro and transplanted CIO cell type enriched genes and regions, (D) developing mouse epithelial cell type marker genes; 3) amino acid substitution rate (dN/dS) and epithelial cell type expression specificity (Tau) of epithelial cell class and specific cell type marker genes; 4) differentially expressed genes (DEG) between species, including (A) human-chimp DEGs of each intestinal epithelial cell type of in vitro or transplanted organoids, (B) human-mouse DEGs of epithelial cell type between developing human and mouse tissues, (C) developing human and mouse tissue DEG along stem-cell-to-enterocyte pseudotime trajectory, (D) human-chimp DEGs based on consensus genome; (E) human-chimp DEGs after stem cell to enterocyte differentiation pseudotime alignment; 5) collected evolutionary selection signatures for composite annotation of open chromatin regions.