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Transcription profile of primordium gut organs

ABSTRACT: Induced pluripotent stem (iPS) cells are a novel stem cell population induced from mouse and human adult somatic cells through reprogramming by transduction of defined transcription factors. Recently, researchers success in generation various cells from iPSCs. Lung progenitor cells are able to differentiate to all of the cells exist in adult lung, attract attention for regenerative medicine. It is known to present between embryonic day 9.5 from 13.5 in mice. We can realized at regenerative medicine in lung using lung progenitor cell surface markers defined by compering each endoderm primordia of organ formation. We investigated the differences in gene expression of each endoderm organ.

ORGANISM(S): Mus musculus

PROVIDER: GSE55312 | GEO | 2014/03/25

SECONDARY ACCESSION(S): PRJNA239304

REPOSITORIES: GEO

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Transcription profile of primordium gut organs

Project description:Induced pluripotent stem (iPS) cells are a novel stem cell population induced from mouse and human adult somatic cells through reprogramming by transduction of defined transcription factors. Recently, researchers success in generation various cells from iPSCs. Lung progenitor cells are able to differentiate to all of the cells exist in adult lung, attract attention for regenerative medicine. It is known to present between embryonic day 9.5 from 13.5 in mice. We can realized at regenerative medicine in lung using lung progenitor cell surface markers defined by compering each endoderm primordia of organ formation. We investigated the differences in gene expression of each endoderm organ. Mouse gut organs morphogenesis begin at E9.5-E11.5. The primordium lung, esophagus, stomach, and intestine at E11.5 were dissected and analysed transcription profile.

2014-03-25 | E-GEOD-55312 | biostudies-arrayexpress

Benary2021 - tissue dynamics of the hepato-pancreato-biliary organ system

Project description:Single cell-based studies have revealed tremendous cellular heterogeneity in stem cell and progenitor compartments, suggesting continuous differentiation trajectories with intermixing of cells at various states of lineage commitment and notable degree of plasticity during organogenesis. The hepato-pancreato-biliary organ system relies on a small endoderm progenitor compartment that gives rise to a variety of different adult tissues, including liver, pancreas, gallbladder, and extra-hepatic bile ducts. Experimental manipulation of various developmental signals in the mouse embryo underscored important cellular plasticity in this embryonic territory. This is also reflected in the existence of human genetic syndromes as well as congenital or environmentally-caused human malformations featuring multiorgan phenotypes in liver, pancreas and gallbladder. Nevertheless, the precise lineage hierarchy and succession of events leading to the segregation of an endoderm progenitor compartment into hepatic, biliary, and pancreatic structures are not yet established. Here, we combine computational modelling approaches with genetic lineage tracing to assess the tissue dynamics accompanying the ontogeny of the hepato-pancreato-biliary organ system. We show that a multipotent progenitor domain persists at the border between liver and pancreas, even after pancreatic fate is specified, contributing to the formation of several organ derivatives, including the liver. Moreover, using single-cell RNA sequencing we define a specialized niche that possibly supports such extended cell fate plasticity.

2021-07-01 | MODEL2105030001 | BioModels

Transcription profile of primordium gut organs

Project description:The mechanisms of gastrointestinal morphogenesis in mammals are not well understood. This is partly due to the lack of organ specific gene expression pattern in the gastrointestinal tract during development. The initiation of organ bud formation occurs at E9.5-E11.5 in mice. These primordia for the digestive organs, including esophagus, stomach, and intestine, protrude from a tube-like structured endoderm, and have their own distinct morphogenesis. Thus, using mouse embryos, we surveyed transcription of prospective these three regions at E11.5 during gastrointestinal morphogenesis. This early digestive organ specific transcription profile will be useful for understanding of the mechanisms of gastrointestinal development.

2012-06-01 | GSE30742 | GEO

Transcription profile of primordium gut organs

2012-05-31 | E-GEOD-30742 | biostudies-arrayexpress

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Endoderm RNA-seq and ChIP-seq data sets]

Project description:Unraveling complex signaling programs animating developmental lineage-decisions is pivotal to differentiate human pluripotent stem cells (hPSC) into pure populations of desired lineages for regenerative medicine. Developmental signals are strikingly temporally dynamic: BMP and Wnt initially specify primitive streak (progenitor to endoderm) yet 24 hours later suppress endoderm and induce mesoderm. At lineage bifurcations we show mutually-exclusive embryonic lineages are segregated through cross-repressive signals: TGFM-NM-2 and BMP/MAPK duel to respectively specify pancreas versus liver from endoderm. Unilateral endodermal differentiation requires blockade of alternative fates at every stage, revealing a universal developmental strategy for efficient differentiation and anterior-posterior patterning of diverse hPSC lines into highly-pure endodermal populations. This culminated in hPSC-derived hepatic progenitors that, for the first time, engraft long-term in genetically-unconditioned mouse livers and secrete human albumin. Finally, thirty transcriptional and chromatin state maps capturing endoderm commitment revealed endodermal enhancers reside in an unanticipated diversity of "pre-enhancer" chromatin states before activation. Endoderm RNA-seq and ChIP-seq data sets

2013-11-22 | E-GEOD-52657 | biostudies-arrayexpress

Metabolomic Profiling of Human Pluripotent Stem Cell Differentiation into Lung Progenitors

Project description:Metabolism is vital to cellular function and tissue homeostasis during human lung development. In utero, embryonic pluripotent stem cells undergo endodermal differentiation towards a lung progenitor cell fate that can be mimicked in vitro using induced human pluripotent stem cells (hiPSCs) to study genetic mutations. To identify differences between wild type and surfactant protein B (SFTPB)-deficient cell lines during endoderm specification towards lung, we used an untargeted metabolomics approach to evaluate the developmental changes in metabolites. We found that the metabolites most enriched during the differentiation from pluripotent stem cell to lung progenitor cell, regardless of cell line, were sphingomyelins and phosphatidylcholines, two important lipid classes in fetal lung development. The SFTPB mutation had no metabolic impact on early endodermal lung development. The identified metabolite signatures during lung progenitor cell differentiation may be utilized as biomarkers for normal embryonic lung development.

2021-06-29 | ST002055 | MetabolomicsWorkbench

Vascularized And Complex Organ Buds From Diverse Tissues Via Mesenchymal Cell-Driven Condensation

Project description:Here, we demonstrate a generalized method for organ bud formation from diverse tissues by combining pluripotent stem cell-derived tissue-specific progenitors or relevant tissue samples with endothelial cells and mesenchymal stem cells (MSCs). The MSCs initiated condensation within these heterotypic cell mixtures, which was dependent upon substrate matrix stiffness. Defining optimal mechanical properties promoted formation of 3D, transplantable organ buds from tissues including kidney, pancreas, intestine, heart, lung, and brain. Transplanted pancreatic and renal buds were rapidly vascularized and self-organized into functional, tissue-specific structures. These findings provide a general platform for harnessing mechanical properties to generate vascularized, complex organ buds with broad applications for regenerative medicine. Gene expression profiles of development-related gene expression in kidney bud transplants and murine kidneys.

2015-07-01 | E-GEOD-66454 | biostudies-arrayexpress

Cellular models of hepatogenesis using embryonic stem cells

Project description:Induced pluripotent stem cells (iPSCs) and human embryonic stem cells (hESCs) can be differentiated into hepatocyte-like cells (HLCs) and thus provide a defined and renewable source for toxicology and regenerative medicine. Critical comparison of patient-specific iPSCs to the golden standard—hESCs will provide an assessment of their strengths and weaknesses. This dataset consists of data at the transcriptional level during the differentiation process of hESCs into HLCs including the definite endoderm (DE) and hepatic endoderm (HE) stages. Besides for the study of this in-vitro-hepatogenesis model, it can be used as reference for investigating the differences and similarities between iPSC and hESC cellular models during hepatogenesis.

2018-01-16 | GSE100447 | GEO

Vascularized And Complex Organ Buds From Diverse Tissues Via Mesenchymal Cell-Driven Condensation

2015-07-01 | GSE66454 | GEO

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Endoderm RNA-seq and ChIP-seq data sets]

Project description:Unraveling complex signaling programs animating developmental lineage-decisions is pivotal to differentiate human pluripotent stem cells (hPSC) into pure populations of desired lineages for regenerative medicine. Developmental signals are strikingly temporally dynamic: BMP and Wnt initially specify primitive streak (progenitor to endoderm) yet 24 hours later suppress endoderm and induce mesoderm. At lineage bifurcations we show mutually-exclusive embryonic lineages are segregated through cross-repressive signals: TGFβ and BMP/MAPK duel to respectively specify pancreas versus liver from endoderm. Unilateral endodermal differentiation requires blockade of alternative fates at every stage, revealing a universal developmental strategy for efficient differentiation and anterior-posterior patterning of diverse hPSC lines into highly-pure endodermal populations. This culminated in hPSC-derived hepatic progenitors that, for the first time, engraft long-term in genetically-unconditioned mouse livers and secrete human albumin. Finally, thirty transcriptional and chromatin state maps capturing endoderm commitment revealed endodermal enhancers reside in an unanticipated diversity of "pre-enhancer" chromatin states before activation.

2013-11-22 | GSE52657 | GEO

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