E-MTAB-1086 - ChIP-seq and RNA-seq of coding RNA of the progression of human embryonic stem cells to beta cells to characterize the epigenetic programs that underlie pancreas differentiation

Status
Released on 8 February 2013, last updated on 3 May 2014
Organism
Homo sapiens
Samples (7)
Protocols (14)
Description
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.
Experiment types
ChIP-seq, RNA-seq of coding RNA, binding site identification, cell type comparison, co-expression, development or differentiation, is expressed
Contacts
Citation
Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells. Xie R, Everett LJ, Lim HW, Patel NA, Schug J, Kroon E, Kelly OG, Wang A, D'Amour KA, Robins AJ, Won KJ, Kaestner KH, Sander M. , Europe PMC 23318056
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1086.idf.txt
Sample and data relationshipE-MTAB-1086.sdrf.txt
Processed data (1)E-MTAB-1086.processed.1.zip
Links