Pancreatic differentiation and specification of lineages is a tightly controlled process involving a interconnected network of transcriptional regulation. Although more knowledge on human pancreatic development is accumulating, the precise role of many transcription factors is only described in mouse. Therefore, it is of great interest to expand our knowledge using alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells. Here, we provide stage-specific data from RNA-, ChIP-, and ATAC-sequencing to dissect transcriptional and regulatory mechanisms during pancreatic development. We provide here genome coverage files and peaks of ATAC-seq, RNA-seq as well as ChIP-seq (ONECUT1 and GATA6) experiments at distinct pancreas differentiation stages. These include hPSCs (ES) from their pluripotent stage towards definitive endoderm (DE) followed by gut tube endoderm (GTE), pancreatic endoderm (PE) and pancreatic progenitors (PP). We also include a IGV (Integrative Genomics Viewer) session (igv_session_rel.xml) for vizualisation of all tracks.