Transcriptional and epigenetic profiling of the progression of hESCs to beta cells

To characterize the epigenetic programs that underlie pancreas differentiation, we have generated genome-scale maps of H3K4me and H3K27me3 patterns by ChIP-seq and determined expression profiles by RNA-seq from undifferentiated human ESCs, four intermediate differentiated stages (definitive endoderm, primitive gut tube, posterior foregut, and pancreatic endoderm), and in vitro-differentiated polyhormonal cells. Antibodies against CD142 and CD200 were used to select for targeted pancreatic and endocrine populations at the end of the culture. Cells at the end of culture were implanted into mice for further differentiation into mature insulin-producing beta-cells and compared to sorted polyhormonal cells by RNA-seq and ChIP-seq analysis. For the experimental factor values the time points are along a differentiation protocol from stem cells to tissue. Values in the CD antibody column refer to antibodies used for cell sorting. In this column 'not applicable' refers to samples that were not sorted. 'none' refers to samples that were sorted, but did not bind to either of the two antibodies, CD200 and CD142. Values in the histone antibody column are about the ChIP process.