Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of gene expression similarity between mouse extrahepatic bile duct and pancreatic duct epithelia and organoids prepared from these epithelia.

ABSTRACT: Comparison of gene expression similarity between mouse extrahepatic bile duct and pancreatic duct epithelia and organoids prepared from these epithelia.

PROVIDER: PRJNA804577 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17951430_1.fastq.gz	Fastqsanger.gz
	SRR17951430_2.fastq.gz	Fastqsanger.gz
	SRR17951431_1.fastq.gz	Fastqsanger.gz
	SRR17951431_2.fastq.gz	Fastqsanger.gz
	SRR17951432_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Comparison of gene expression similarity between mouse extrahepatic bile duct and pancreatic duct epithelia and organoids prepared from these epithelia.

Project description:By RNA sequencing we found that extrahepatic bile duct organoids and pancreatic duct organoids have similar gene expression signatures compared with duct epithelia.

2023-06-06 | GSE196394 | GEO

Human bile cholangiocyte organoids originate from the extrahepatic bile duct and can repair bile duct scaffolds in vitro

Project description:Cholangiocyte organoids provide a powerful tool for characterizing bile duct epithelium and expanding cholangiocytes for tissue engineering purposes. However, this involves invasively obtained tissue-biopsies via surgery which is not preferential and limits the patient-specific capacities of these cultures. To overcome this, organoid culture were initiated from minimal invasive bile-samples obtained during routine clinical procedures. Characterization revealed that these bile-cholangiocyte organoids originate from the extrahepatic bile duct and are capable to repopulate human extrahepatic bile duct scaffolds. With this, bile duct tissue engineering as well as personalized disease modelling is in sight.

2020-11-19 | GSE156519 | 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

Molecular classification and therapeutic targets in extrahepatic cholangiocarcinoma

Project description:Genome-wide expression analysis of 182 extrahepatic cholangiocarcinoma and 38 non-tumoral bile duct samples as part of a integrated study of gene expression and targeted DNA-sequencing in patients with extrahepatic cholangiocarcinoma We used whole-genome transcriptome to conduct an unsupervised molecular classification of extrahepatic cholangiocarcinoma

2020-03-22 | GSE132305 | GEO

Human bile cholangiocyte organoids originate from the extrahepatic bile duct and can repair bile duct scaffolds in vitro

Project description:Human bile cholangiocyte organoids originate from the extrahepatic bile duct and can repair bile duct scaffolds in vitro

| PRJNA658150 | ENA

Distinct Phenotypes of Human Intrahepatic and Extrahepatic Bile duct Organoids and their Applications for Biliary Disease Modeling

Project description:Bile draining by the bile duct system is paramount for good liver function. Diseases which compromise the integrity of the biliary tree are common and often life-threatening. Both intrahepatic and extrahepatic bile ducts contain distinct (stem) cell niches which are important for bile duct homeostasis and repair. A detailed characterization of the cell populations in the extrahepatic bile ducts has been lacking due to the inability of cell culture propagation. The aim of this study was to expand extrahepatic bile duct stem cells using the organoid culture system developed for intrahepatic bile duct cells. Extrahepatic bile duct (eBD)-organoids and intrahepatic (iBD) liver-derived organoids were initiated from paired biopsies of human common bile duct and liver tissue. Organoids of both origins were characterized on the basis of morphology and growth characteristics, gene and protein expression profiles, and their differentiation capacity towards mature cholangiocytes and hepatocytes. Although eBD organoids were very similar to iBD liver organoids, some differences in growth rate, organoid size and gene and protein expression were found. More strikingly, although both organoids could be differentiated towards a mature cholangiocyte phenotype, only iBD organoids can be directed to a mature hepatocyte phenotype. Of note, eBD organoids derived from a cystic fibrosis (CF) patient, harboring the same CFTR mutation (dF508-R1162X) as found in the patient, showed normal Ca2+-dependent Cl- channel and MDR-1 transporter activity but no CFTR channel activity. In conclusion, we here show feasibility of expanding eBD organoids with distinct properties when compared to iBD organoids. These eBD organoids may provide an excellent model for studying bile duct diseases and regenerative medicine.

| EGAS00001003792 | EGA

Transcription profiling of undifferentiated human extrahepatic cholangiocyte organoids (ECOs)

Project description:3D cell culture systems (organoids), cultured from extrahepatic bile duct biopsies, resemble biliary epthelium (cholangiocytes) upon culture according to the protocol previously established for culturing intrahepatic cholangiocyte organoids from liver biopsies (Huch et al. Cell 2015). These extrahepatic cholangiocyte organoids (ECOs) in Canonical-Wnt culture conditions maintain their genetic stability, and transcription profile and can be maintained and propagated during long periods of culturing while still maintaining their functional properties. The data presented in this ArrayExpress submission contained micro array results of 3 different ECO lines that were analyzed for their functional cholangiocyte ion-channels, involved in secreting a protective bicarbonate layer. It was shown that these data closely resemble the expression profile of intrahepatic cholangiocyte organoids (ICOs) as described by our group. Results of the ICOs are deposited in the EMBL-EBI ArrayExpress repository under number E-MTAB-9044.

2021-01-01 | E-MTAB-9807 | biostudies-arrayexpress

Effect of bile duct ligation on growth factors expression from mouse whole extrahepatic bile duct (EHBD) tissue and cultured mouse neonatal fibroblasts and bile duct organoids

Project description:Effect of bile duct ligation on growth factors expression from mouse whole extrahepatic bile duct (EHBD) tissue and cultured mouse neonatal fibroblasts and bile duct organoids

| PRJNA754373 | ENA

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

Single-cell RNA-seq of total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- and Pou2f3+/+, Pou2f3+/- mice

Project description:Total gallbladder/extrahepatic duct tissue digest from Pou2f3-/- (KO) and Pou2f3+/+, Pou2f3+/- (heterozygous and homozygous WT mice together in WT sample) littermated mice were sorted for live cells on Moflo XDP cell sorter (singlets, FSCAxSSCA, DAPI-). Immediately post-sorting, cells were run on 10X Chromium (10X Genomics) and then through library preparation by the Institute for Human Genetics at UCSF following the recommended protocol for the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry). Libraries were run on the NovaSeq 6000 for Illumina sequencing. Post-processing and quality control were performed by the Genomics Core Facility at the Institute for Human Genetics at UCSF using the 10X Cell Ranger package (Cell Ranger Version 3.0.2, 10X Genomics). Primary assessment with this software for WT DC sample reported 2,441 cell-barcodes with 7,651 median unique molecular identifiers (UMIs, transcripts) per cell and 2,004 median genes per cell sequenced to 61.4% sequencing saturation with 48,559 mean reads per cell. Primary assessment with this software for MARCH1-/- DC sample reported 681 cell-barcodes with 6,309 median unique transcripts per cell and 1,774 median genes per cell sequenced to 73.1% sequencing saturation with 202,410 mean reads per cell.

2022-03-01 | GSE196546 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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