Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA-seq of Sox9-deficient intrahepatic biliary epithelial cells

ABSTRACT: To define the regulatory role of Sox9 in intrahepatic biliary epithelium, we conducted bulk RNA-seq on biliary epithelial cells (BECs) from adult control (Sox9fl/fl) and conditional Sox9 knockout (Sox9cKO; Sox9fl/fl:Albumin-Cre) mice. Livers were dissociated to single cells and BECs isolated by FACS based on CD326 positivity. CD31+ and CD45+ cells were excluded by FACS. Gallbladder and extrahepatic tissues were excluded by dissection. RNA was isolated using Ambion RNAqueous Micro kit and libraries were made using Takara SMARTer Stranded Total RNA-seq Kit v3 Pico.

ORGANISM(S): Mus musculus

PROVIDER: GSE249385 | GEO | 2024/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-seq of Sox9-deficient intrahepatic biliary epithelial cells

Project description:To define the regulatory role of Sox9 in intrahepatic biliary epithelium, we conducted single cell RNA-seq on biliary epithelial cells (BECs) from adult control (Sox9fl/fl) and conditional Sox9 knockout (Sox9cKO; Sox9fl/fl:Albumin-Cre) mice. Livers were dissociated to single cells and BECs isolated by FACS based on CD326 positivity. CD31+ and CD45+ cells were excluded by FACS. Gallbladder and extrahepatic tissues were excluded by dissection. Sorted cells were fixed according to manufacturer instructions using Parse Whole Cell Fixation kit. Fixed cells were frozen and stored at -70C for less than 6mo, prior to being used in split-pool combinatorial barcoding according to manufacturer instructions. Barcoding and library construction was carried out with the Parse Evercode Whole Transcriptome v2 kit.

2024-01-01 | GSE249558 | GEO

RNA-seq of intrahepatic Sox9EGFP populations

Project description:Cellular heterogeneity in the biliary epithelium is poorly understood, and genetic biomarkers for identifying distinct biliary epithelial cell (BEC) subpopulations are limited. Here, we utilized a Sox9EGFP transgene to study cellular heterogeneity in intrahepatic BECs. Male Sox9EGFP mice were fasted overnight, and livers were dissociated to obtain single cells. Gallbladders and extrahepatic ducts were excluded by dissection. Sox9EGFP populations were isolated by FACS into four distinct populations: GFPnegative, GFPsublow, GFPlow, and GFPhigh. We conducted RNA-seq and differential gene expression analysis to identify genes shared between and unique to each population.

2020-05-29 | GSE151387 | GEO

Transcriptional profiles of biliary epithelial cells from non-pregnant mice and pregnant mice at dpc8

Project description:We report transcriptional profiles of liver biliary epithelial cells (BECs) from non-pregnant mice and pregnant mice. By RNA-sequencing of FACS-isolated BECs, we revealed that genes related to tissue morphogenesis and actin cytoskeleton were upregulated on dpc8.

2023-04-01 | GSE189873 | GEO

Transcriptional profiling of hepatocyte, reprogrammed hepatocyte, and biliary cells

Project description:Following liver injury, a subset of hepatocytes adopt features of biliary epithelial cells (BECs) in a process known as biliary reprogramming. The aim of this study is to elucidate the molecular events accompanying this dramatic shift in cellular identity. Wild type hepatocytes, wild type biliary cells, DDC-treated hepatocytes, DDC-treated biliary cells, and DDC-treated reprogrammed cells were isolated by FACS, RNA isolated, and sequenced.

2020-08-27 | GSE156894 | GEO

Expression data of mesenchymal cells from mouse liver

Project description:There are a few markers available to distinguish hepatic stellate cells (HSCs), portal fibroblasts (PFs), and mesothelial cells (MCs) in the adult mouse liver. To identify genes uniquely expressed in these cells, we isolated HSCs having Vitamin A lipids by FACS based on their autofluorescence. We isolated a mixed population containing PFs and MCs as Vitamin A lipid-negative and GFP-positive cells by FACS from Collagen1a1 promoter-driven GFP transgenic mice. MCs were isolated by FACS using anti-GPM6A antibodies from adult mouse livers. PFs were isolated by FACS as Vitamin A lipid-negative, GFP-positive, and GPM6A-negative cells. We also isolated HSCs, MCs, and PFs from Collagen1a1 promoter-driven GFP transgenic mouse livers having biliary fibrosis by FACS. Biliary fibrosis was induced by bile duct ligation for 3 weeks. Sham operation was performed as a control. After separation of these cells, we isolated total RNAs and analyzed mRNA expression by microarray analysis. Total RNA was extracted with RNAqueous Micro (Ambion) and the probes for the microarray were synthesized using the Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin module V2 (Nugen). The labeled probes were hybridized with GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) and signals were analyzed with Genomic Suite software (Partek).

2016-03-11 | E-GEOD-66788 | biostudies-arrayexpress

Downregulation of TGR5 (GPBAR1) in biliary epithelial cells is characteristic of sclerosing cholangitis and may contribute to disease pathogenesis

Project description:Primary sclerosing cholangitis (PSC) is characterized by chronic inflammation and progressive fibrosis of the biliary tree. The bile acid receptor TGR5 is found on biliary epithelial cells (BECs), where it promotes secretion, proliferation and tight junction integrity. Thus, we speculated that changes in TGR5 expression in BECs may contribute to PSC pathogenesis.

2021-03-12 | GSE168758 | GEO

Gene expression profiling of ampullary carcinomas classifies ampullary carcinomas into biliary-like and intestinal-like subtypes that are prognostic of outcome

Project description:Adenocarcinomas of the ampulla of Vater are classified as biliary cancers, though the exact epithelium of origin for these cancers is not known. We sought to molecularly classify ampullary adenocarcinomas in comparison to known adenocarcinomas of the pancreas, extrahepatic bile duct, and duodenum by gene expression analysis. We analyzed 32 fresh-frozen resected, untreated periampullary adenocarcinomas (8 pancreatic, 2 extrahepatic biliary, 8 duodenal, and 14 ampullary) using the Affymetrix U133 Plus 2.0 genome array.

2013-01-01 | E-GEOD-39409 | biostudies-arrayexpress

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

MiRNA expression in embryonic murine hepatocytes versus murine cholangiocytes at E18.5

Project description:Differentially expressed miRNAs between hepatocytes (GFP-neg in SOX9-GFP mice) and cholangiocytes (GFP-pos in SOX9-GFP mice) in mice at E18.5. We want to compare miRNA population in biliary cells and parenchymal cells (depleted from hematopoietic cells) during liver development. Cholangiocytes specifically express the transcription factor Sox9. This enables to separate cholangiocytes from the rest of the liver parenchyma by FACS from Sox9-GFP transgenic mice. In conclusion, we want to compare miRNA population in our GFP+ cells (cholangiocytes) and our GFP- cells (liver parenchyma depleted from hematopoietic cells).

2018-12-20 | GSE100145 | GEO

Simultaneous activation of Kras-Akt and Notch pathways induces extrahepatic biliary cancer via mTORC1 pathway

Project description:Biliary tract cancer (BTC) has poor prognosis. The Notch receptor is aberrantly expressed in extrahepatic cholangiocarcinoma (eCCA). However, the role of Notch signaling in the initiation and progression of eCCA and gallbladder (GB) cancer remains unknown. We investigated the functional role of Notch signaling during tumorigenesis of the extrahepatic bile duct and GB. We demonstrated that simultaneous activation of the Kras–Akt and Notch pathways in EHBD and GB resulted in the formation of BilINs and biliary cancer in a mouse model. Mechanistically, the Kras/Notch–Myc axis activates mTORC1 through phosphorylation of TSC2 in biliary tumorigenesis.

2023-05-04 | GSE231369 | GEO

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