Collections / geo-gse306111

geo-gse306111

Datasets4
Size~3.8 GB
TechnologyCosMx SMI
Samplehuman · liver
KindPublication
Flag a data issue
10.1053/j.gastro.2025.11.014 ↗
Python · sddb client
from sddb import Catalog

cohort = Catalog().collection("geo-gse306111")
cohort.members        # the 4 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse306111")
coll.ordered_artifacts.to_dataframe()   # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse306111 --dest data/

Licenses: 4 NCBI GEO policy

Activation of the Integrin αV-YAP-CTGF Axis in Liver Sinusoidal Endothelial Cells Promotes Liver Fibrogenesis, Leading to Portal Hypertension and Liver Carcinogenesis in Congestive Hepatopathy.

<h4>Background & aims</h4>Chronic liver congestion progresses to liver fibrosis, eventually leading to cirrhosis and cancer. This study aimed to elucidate the mechanism of congestive hepatopathy (CH), focusing on liver sinusoidal endothelial cells (LSECs).<h4>Methods</h4>Partial inferior vena cava ligation (pIVCL) was performed to induce hepatic congestion in mice. Single-cell RNA sequencing (scRNA-seq) was conducted on murine livers after pIVCL. Cells underwent hydrostatic pressure stimulation. scRNA-seq and spatial transcriptomics were performed on human livers from patients with Fontan-associated liver disease.<h4>Results</h4>The scRNA-seq analysis showed that the integrin signaling pathway and yes-associated protein (YAP) were activated in pericentral LSECs after pIVCL. The most upregulated gene in pericentral LSECs was connective tissue growth factor (CTGF). Hydrostatic pressure activated YAP through integrin αV, leading to the upregulation of CTGF and type IV collagen (COL4) expression in LSECs. LSEC-derived CTGF upregulated the type I collagen (COL1) and COL4 expression in hepatic stellate cells. CTGF knockout in endothelial cells ameliorated CH-induced liver fibrosis and portal hypertension and even suppressed liver tumorigenesis. Integrin αV inhibition alleviated CH-induced liver fibrosis and portal hypertension with the decreased expression of CTGF, COL4, and COL1. scRNA-seq and spatial transcriptomics of clinical Fontan-associated liver disease samples revealed YAP activation and CTGF upregulation in pericentral LSECs, potentially leading to increased COL4 expression in LSECs and increased COL1 expression in hepatic stellate cells as fibrosis progressed.<h4>Conclusions</h4>CTGF induction in LSECs may play an upstream role in the fibrogenesis of CH. The integrin αV-YAP-CTGF axis in LSECs could be a potential therapeutic target for CH.

Open in Vitessce
CosMx SMI
Human liver
GSM9193450
human liver 1.5 GB 289,129 cells bronze NCBI GEO policy
TechnologyCosMx SMI
Organismhuman
Tissueliver
Size1.5 GB
Cells289,129
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
CosMx SMI
Human liver
GSM9309756
human liver fontan-associated liver disease 233 MB 46,975 cells bronze NCBI GEO policy
TechnologyCosMx SMI
Organismhuman
Tissueliver
Conditionfontan-associated liver disease
Size233 MB
Cells46,975
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
CosMx SMI
Human liver
GSM9193452
human liver fontan-associated liver disease 645 MB 215,573 cells bronze NCBI GEO policy
TechnologyCosMx SMI
Organismhuman
Tissueliver
Conditionfontan-associated liver disease
Size645 MB
Cells215,573
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
CosMx SMI
Human liver
GSM9193451
human liver fontan-associated liver disease 1.4 GB 241,700 cells bronze NCBI GEO policy
TechnologyCosMx SMI
Organismhuman
Tissueliver
Conditionfontan-associated liver disease
Size1.4 GB
Cells241,700
bronze NCBI GEO policy Open in Vitessce

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No linked publication found — please cite the data source.