Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina Genome Analyzer IIx, Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Maike Sander

PROVIDER: E-MTAB-1086 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells.

Xie Ruiyu R Everett Logan J LJ Lim Hee-Woong HW Patel Nisha A NA Schug Jonathan J Kroon Evert E Kelly Olivia G OG Wang Allen A D'Amour Kevin A KA Robins Allan J AJ Won Kyoung-Jae KJ Kaestner Klaus H KH Sander Maike M

Cell stem cell 20130111 2

Embryonic development is characterized by dynamic changes in gene expression, yet the role of chromatin remodeling in these cellular transitions remains elusive. To address this question, we profiled the transcriptome and select chromatin modifications at defined stages during pancreatic endocrine differentiation of human embryonic stem cells. We identify removal of Polycomb group (PcG)-mediated repression on stage-specific genes as a key mechanism for the induction of developmental regulators. ...[more]

PMID: 23318056

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Project description:The Interleukin-22 (IL22) pathway plays a key role in maintaining homeostasis at the mucosal surfaces and is frequently dysregulated during infectious and inflammatory diseases. Human genome-wide association studies performed at the WTSI have identified SNPs in and around the human IL-22 gene that are associated with IBD susceptibility. The IL-22 cytokine is produced by cells of the innate and adaptive immune systems within the intestinal mucosa and acts on the IL-22 receptor (IL-22RA1) that is present specifically on intestinal epithelial cells. Studies to date have shown the that IL-22 pathway is linked to proliferative and anti-apoptotic pathways, as well as anti-microbial molecule production that help control bacterial invasion and prevent tissue damage. We are characterizing a novel IL-22RA1 KO mouse and have shown that these mice are highly susceptible to enteric bacterial pathogens, such as Citrobacter rodentium and Clostridium difficile. However, the mechanism of this protective immunity is poorly understood. The aim of this project is to identify novel molecules or pathways downstream of IL-22 signaling that provide the mechanistic link between IL-22RA1 and innate immunity. To maintain mouse colonic epithelial cells in vitro, we used an organoid culture system that faithfully recapitulates the crypt architecture of the gastrointestinal epithelium. Primary colonic epithelial crypts were isolated from age-matched wildtype and IL-22ra1 knock-out mice (n = 4 per genotype), and subsequently cultured in the presence of defined growth factors and Matrigel for 5 days. The resulting mature organoids were then either treated with Control medium (Advanced DMEM/F12) or mouse recombinant IL-22 (50ng/ml) for 16 hours. Total RNA were extracted using the QIAgen RNeasy Micro Kit, including an on-column DNAse digestion step, according to manufacturer's protocol. We are submit total RNA samples of good quality (RIN > 7) and quantity.The culture and stimulation conditions have been optimised to achieve significant and specific induction of known target genes such as the antimicrobial peptides RegIIIb, RegIIIg, S100a8 and S100a9. Two technical replicates will be available for each genotype x condition. We aim to sequence 5GBp per replicate, and 5 replicates per lane on an Illumina platform. Through this dataset, we hope to discover epithelial cell-specific pathways downstream of IL-22 signaling that are ablated in the absence of its receptor.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Dataset Information

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

Publications

Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells.

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