In the version of this Article originally published, text referencing ATAC-seq data was incorrectly retained. References to ATAC-seq data, which are not included in this study, should be removed from the text in the Results sections ‘In vitro-generated definitive endoderm forms by partial EMT’ and ‘Foxa2 suppresses a complete EMT during endoderm formation’, as well as from the author contributions section. The Methods subsection ‘ChIP-seq and ATAC-seq data visualization’ should also be completely removed. The errors have been corrected.