Distinct gene expression signatures in human embryonic stem cells differentiated towards definitive endoderm at single-cell level

► Human embryonic stem cells can potentially be used to generate any cell type. ► Three protocols to generate definitive endoderm in vitro were evaluated. ► Cell differentiation can be monitored by gene expression profiling. ► A combination of biomarkers needs to be used to characterize definitive endoderm. ► Single-cell analysis reveal distinct cell characteristics for differentiated cells.