GEO DataSets

(Submitter supplied) The goal of this experiment was to analyse transcriptomic changes between Biliary epithelial cells or BECs from the liver of mice treated with Acetaminophen (a drug that causes acute liver injury) in combination with AAV8-Tbg-p21 viral vector to induce hepatocyte senecence. The aim was to understand the impact of injury on transcriptional status of biliary epithelial cells. Briefly, we analyzed mouse liver cells (hepatocytes and non-parenchymal cells fractions) obtained by in-situ liver perfusion 48 h after injury. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

4 Samples

Download data: H5

(Submitter supplied) Identify differentially expressed genes in small mice cholangiocyte cell line (SMCC) when CTNNB1 is activated or silenced.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

12 Samples

Download data: CSV, WIG

(Submitter supplied) In other to assess functional involvement of Klf5 in DR regulation, we made liver-specific Klf5 knockout mice. Ductular reaction upon cholestatic liver injury is severely suppressed in these mice. We conducted RNA-seq analysis on the BECs from control mice and Klf5 LKO mice upon DDC injury to further elucidate the Klf5 functions.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration The liver is an essential organ with compartmentalized metabolic processes and significant regenerative capabilities. Repopulation of the liver parenchyma can transpire from both main epithelial cell types, hepatocytes and biliary epithelial cells (BECs). Here, we harness high-throughput single-cell RNA sequencing (scRNA-seq) to dissect the transcriptional heterogeneity and cellular diversity of these epithelial compartments in homeostasis and injury. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV, TXT

(Submitter supplied) Background and Aims: During severe or chronic hepatic injury, biliary epithelial cells (BECs), also known as cholangiocytes, undergo rapid reprogramming and proliferation, a process known as ductular reaction (DR), and allow liver regeneration by differentiating into both functional cholangiocytes and hepatocytes. While DR is a hallmark of chronic liver diseases, including advanced stages of non-alcoholic fatty liver disease (NAFLD), the early events underlying BEC activation are largely unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

12 Samples

Download data: TAB

(Submitter supplied) RNAseq analysis between cell types. RNA extracted using Qiagen mini total RNA isolation protocols (Qiagen, Germany). Samples were treated with DNase (Ambion), and sample integrity verified on the Agilent Bioanalyser with the RNA Nano chip. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out by on a NextSeq-550 sequencer (Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, Scotland, UK). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

12 Samples

Download data: BW

(Submitter supplied) The study used next-generation sequencing to compare mRNA content of EVs from 3 different cell origins which are untreated control or treated with LNP containing VEGFA mRNA. Our goal is to carry out functional and pathway analysis of the differentially expressed genes. The RNA profiles of EV content from treated and untreated cells; lung epithelial (HTB-177) , umbilical vein endothelial (HUVEC), and cardiac progenitor cells(CPC), were generated by RNA-Seq using Illumina NovaSeq6000. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

22 Samples

Download data: TSV

(Submitter supplied) To elucidate the role of PPARα activation in liver progenitor cell-mediated liver regeneration, we used Tg(fabp10a:pt-β-catenin) zebrafish transgenic line where liver progenitor cell-mediated liver regeneration is induced by oncogene overexpression

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

6 Samples

Download data: TXT

(Submitter supplied) Single cell sequencing was performed on the adult zebrafish liver, on both uninjured animals, and animals regenerating from hepatocyte ablation.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

28 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

16 Samples

Download data: MTX, TSV

(Submitter supplied) Biliary epithelial cells (BECs) form bile ducts in the liver, and are facultative liver stem cells that establish a ductular reaction (DR) to support liver regeneration following injury. Liver damage induces periportal LGR5+ putative liver stem cells which can form BEC-like organoids, suggesting RSPO-LGR4/5-mediated WNT/β-catenin activity is important for a DR. We addressed the roles for this and other signaling pathways in a DR by performing a focused CRISPR-based loss-of-function screen in BEC-like organoids, followed by in vivo validation and single-cell RNA sequencing. more...

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL17021 GPL19604

6 Samples

Download data: CSV

(Submitter supplied) The mRNA-based therapeutics such as COVID-19 vaccines are rapidly progressing into the clinic with a tremendous potential of benefiting millions of people worldwide. Therapeutic targeting of injuries that require transient restoration of proteins by mRNA delivery is an attractive aspect, however until recently, it has remained poorly explored. In this study, we examined for the first time therapeutic utility of mRNA delivery in liver fibrosis and cirrhosis, which contributes to millions of deaths, annually. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

2 Samples

Download data: CSV

(Submitter supplied) We previously showed that severe liver diseases are characterized by expansion of liver progenitor cells (LPC), which correlates with disease severity. However, the origin and role of LPC in liver physiology and in the hepatic response to injury remains a contentious topic. We have now used genetic lineage tracing of Hnf1β-expressing biliary duct cells to assess their contribution to LPC expansion and hepatocyte generation during normal liver homeostasis, and following different types of liver injury. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17791

11 Samples

Download data: CEL

(Submitter supplied) Currently, much effort is directed to the development of new cell sources for clinical therapy using cell fate conversion approaches by small molecules. Direct lineage reprogramming to a progenitor state has been reported in terminally differentiated rodent hepatocytes, yet remains a challenge in human hepatocytes. Human hepatocytes were isolated from healthy and diseased donor livers and reprogrammed into progenitor cells by two small molecules, A83-01 and CHIR99021 (AC), in the presence of EGF and HGF. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

7 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TSV

(Submitter supplied) Hepatocytes are considered as a heterogenous cell population in the liver. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of hepatocytes in livers under different feeding conditions.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: MTX, TSV