Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of embryonic cholangiocytes

ABSTRACT: Purpose: The aim of this study is to propose a computational model which can help in unravelling the mechanisms of initial bile duct lumen formation. Guided by the quantification of morphological features and expression of genes in developing bile ducts (cholangiocytes) from embryonic mouse liver, hypotheses for the mechanisms of biliary lumen formation were generated and tested with the model. Here, the RNA-sequencing data were collected from purified embryonic cholangiocytes at two developmental stages (E16 and E18).

ORGANISM(S): Mus musculus

PROVIDER: GSE163062 | GEO | 2021/05/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Plant toxin treatment of neonatal mouse cholangiocytes

Project description:Extrahepatic bile ducts were isolated from mouse pups at days 0-3 and primary cholangiocytes were isolated. Cholangiocytes were treated with DMSO, bilatresone (TOX4), betavulgarin (TOX2), and isoflavanone (TOX3), as per Lorent et al, Science Translationa Medicine 2015;286:286ra67 (Fig. 1), all in DMSO. Treatment concentrations were 2.0 micrograms/ml, for 6 hours.

2020-01-01 | GSE136895 | GEO

De novo formation of a functional biliary system by TGFβ-mediated hepatocyte transdifferentiation

Project description:We observed de novo formation of peripheral bile ducts by transdifferentiation of hepatocytes in mice born without peripheral bile ducts. To assess the authenticity and maturity of the hepatocyte-derived peripheral cholangiocytes forming the new bile ducts, we compared their global gene expression profile to that of peripheral cholangiocytes isolated from normal mice. We also included hepatocytes isolated from mice born without peripheral bile ducts as a control.

2018-05-14 | GSE108315 | GEO

Comparison of extrahepatic cholangiocyte organoids and freshly isolated common bile duct cholangiocytes

Project description:Despite the impact of bile duct disorders, treatment options remain very limited. Poor access to biliary tissue and restrictions in long-term culture or significant expansion of primary cholangiocytes have posed major challenges for research in the field. These limitations have so far precluded large scale experiments such as transcriptomic and genome-wide analyses which are urgently needed to better understand biliary physiology and pathophysiology. To address this issue, we have developed a novel system for the isolation and propagation of primary cholangiocytes from the extrahepatic bile ducts. The resulting Extrahepatic Cholangiocyte Organoids (ECOs) maintain their genetic stability, transcriptomic profile and function over long term culture and are compatible with regenerative medicine applications such as biliary reconstruction. We established a novel protocol for the isolation and propagation of primary cholangiocytes from the extrahepatic biliary tree in the form of extrahepatic cholangiocyte organoids (ECOs). The aim of this experiment was to provide in depth characterisation of the transcriptome of ECOs during long term culture. We compare the transcriptome of ECOs cultured for 1 passage (P1), 10 passages (P10) and 20 passages (P20) with freshly isolated primary cholangiocytes from the common bile duct. Embryonic Stem Cells (ES) cells are used as a negative control=

2017-07-04 | E-MTAB-4591 | biostudies-arrayexpress

Differential gene expression profiling of cultured neu-transformed versus spontaneously-transformed rat cholangiocytes and of corresponding cholangiocarcinomas

Project description:Characterization of preclinical models of intrahepatic cholangiocarcinoma progression that reliably recapitulate altered molecular features of the human disease. Here, we performed comprehensive gene expression profiling of cholangiocarcinoma tumors arising from bile duct inoculation of different grade malignant rat cholangiocytes. Tumors arising from bile duct inoculation of spontaneously-transformed low grade malignant rat BDE1 cholangiocytes (BDEsp cells) compared to tumors arising from the inoculation of high grade malignant erbB-2/neu- transformed BDE1 cholangiocytes (BDEneu cells) into the livers of syngeneic rats.

2012-06-20 | E-GEOD-38834 | biostudies-arrayexpress

Human branching cholangiocyte organoids recapitulate embryogenic bile duct development and provide an unique model to study biliary diseases. RNA-Seq

Project description:Although providing promising and unique tools for studying cholangiocytes, current tissue-derived cholangiocyte-organoid systems do not recapitulate the complex architecture of the intrahepatic bile ducts in vitro. Here, we report a new method for creating branching cholangiocyte organoids (BRCO) from human adult tissue to study the intrahepatic biliary tree and diseases. BRCOs self-organize into large complex tubular structures, while closely resembling primary cholangiocytes on a transcriptomic and functional level. They are capable of mimicking branching bile duct development as well as being used for studying diseases in which the biliary tree does not develop properly (Alagille Syndrome). Furthermore, we deliver evidence that our culture method allows for formation of complex cholangiocyte cancer (cholangiocarcinoma, CCA) organoids. These branching CCA organoids resemble the primary tumor more closely compared to previously published protocols as well as showing unique tumor-specific drug responses. In conclusion, our culture method allows for creation of novel (malignant) cholangiocyte-organoids to study the intrahepatic bile ducts.

2022-05-04 | GSE179599 | GEO

Human branching cholangiocyte organoids recapitulate embryogenic bile duct development and provide an unique model to study biliary diseases. scRNA-Seq

2022-05-04 | GSE179597 | GEO

Proteome of human branching and non-branching cholangiocyte organoids

Project description:Current model systems for studying intrahepatic biliary disease fail to recapitulate the architecture of intrahepatic bile ducts. Organoids from intrahepatic cholangiocytes can with a new culture method grow with a branching pattern resembling the structure of intrahepatic bile ducts. This dataset contains data from samples of these organoids and from control organoids cultured without this technique. Culture have been performed using isotope labeled amino acids to help distinguish cell derived proteins from the basement membrane extract used as a culture substrate for the organoids.

2022-05-09 | PXD028532 | Pride

Transcriptome analysis of embryonic cholangiocytes

Project description:Transcriptome analysis of embryonic cholangiocytes

| PRJNA684581 | ENA

Interaction with Cholangiocytes and Neutrophils

Project description:Alcoholic hepatitis (AH) is a life-threatening disease with limited treatment options. The presence of cholestasis worsens prognosis but the responsible mechanism is unknown. AH results in infiltration of polymorphonuclear neutrophils (PMNs) in the liver, and cholestasis often reflects bile duct pathology, so we investigated whether and how PMNs interact with cholangiocytes in AH.

2020-03-13 | GSE146899 | GEO

Reprogramming fibroblasts into bi-potential hepatic stem cells by defined factors

Project description:Recent studies have demonstrated direct reprogramming of fibroblasts into a range of somatic cell types, but to date stem/progenitor cells have only been reprogrammed for the blood and neuronal lineages. We previously reported generation of induced hepatocyte-like (iHep) cells by transduction of Gata4, Hnf1α, and Foxa3 in p19 Arf null mouse embryonic fibroblasts (MEFs). Here, we show that Hnf1β and Foxa3, liver organogenesis transcription factors, are sufficient to reprogram MEFs into induced hepatic stem cells (iHepSCs). iHepSCs can be stably expanded in vitro and possess the potential of bi-directional differentiation into both hepatocytic and cholangiocytic lineages. In the injured liver of fumarylacetoacetate hydrolase (Fah)-deficient mice, repopulating iHepSCs become hepatocyte-like cells. They also engraft as cholangiocytes into bile ducts of mice with DDC-induced bile ductular injury. Lineage-conversion into bi-potential expandable iHepSCs provides a strategy to enable efficient derivation of both hepatocytes and cholangiocytes for use in disease modeling and tissue engineering. iHepSCs were converted form fibroblasts by transduction of Hnf1β and Foxa3. iHepSCs were induced to differentiate into hepatocyte-like cells and cholangiocytes in vitro. Totally, 9 samples including four clones of iHepSCS, one clone of LEPCs, two samples of MEFs and two samples of iHepSCs-derived cholangocytes were analyzed.

2013-07-19 | E-GEOD-48486 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data