Collections / Blocking the Gut–Liver IgA Axis Attenuates Macrophage-Mediated Inflammation and Injury in Alcohol-Associated Liver Disease [Spatial Transcriptomics]

Blocking the Gut–Liver IgA Axis Attenuates Macrophage-Mediated Inflammation and Injury in Alcohol-Associated Liver Disease [Spatial Transcriptomics]

We profiled spatial gene expression in mouse liver and intestine FFPE tissue sections using the 10x Genomics Visium Spatial Gene Expression for FFPE (v2, Mouse) platform. Samples included control and ethanol-fed groups with or without fingolimod (FTY720). Processed data include spatially resolved gene-by-spot count matrices generated by Space Ranger.

Datasets15

Size~499 MB

AssayVisium

Samplemouse · multiple

KindComparison

Flag a data issue

www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE320442 ↗

Download the whole collection

Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse320442")
cohort.members        # the 15 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/")

Install (Python 3.12+) Docs →

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-gse320442")
coll.ordered_artifacts.to_dataframe()   # the 15 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

Install (Python 3.12+) Docs →

Shell

# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse320442 --dest data/

Install (Python 3.12+) Docs →

Licenses: 15 NCBI GEO policy

Member datasets · 15

Visium

Mouse liver

GSM9824771

mouse liver alcoholic liver diseases 32.7 MB 1,751 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditionalcoholic liver diseases

Size32.7 MB

Spots1,751

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9824773

mouse liver alcoholic liver diseases 29.1 MB 1,813 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditionalcoholic liver diseases

Size29.1 MB

Spots1,813

silver H&E NCBI GEO policy

Visium

Mouse intestine

GSM9824766

mouse intestine 48.0 MB 2,905 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueintestine

Size48.0 MB

Spots2,905

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9824767

mouse liver 30.1 MB 1,744 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Size30.1 MB

Spots1,744

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9824774

mouse liver alcoholic liver diseases 31.8 MB 1,669 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditionalcoholic liver diseases

Size31.8 MB

Spots1,669

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9543401

mouse liver alcoholic liver diseases 25.5 MB 1,646 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditionalcoholic liver diseases

Size25.5 MB

Spots1,646

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9543399

mouse liver alcoholic liver diseases 29.6 MB 1,989 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditionalcoholic liver diseases

Size29.6 MB

Spots1,989

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9543397

mouse liver 32.1 MB 2,214 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Size32.1 MB

Spots2,214

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9824770

mouse liver alcoholic liver diseases 32.8 MB 2,048 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditionalcoholic liver diseases

Size32.8 MB

Spots2,048

silver H&E NCBI GEO policy

Visium

Mouse intestine

GSM9824772

mouse intestine 43.9 MB 2,708 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueintestine

Size43.9 MB

Spots2,708

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM9824768

mouse liver 29.0 MB 1,762 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Size29.0 MB

Spots1,762

silver H&E NCBI GEO policy

Visium

Mouse intestine

GSM9543398

mouse intestine 36.4 MB 2,489 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueintestine

Size36.4 MB

Spots2,489

silver H&E NCBI GEO policy

Visium

Mouse intestine

GSM9543396

mouse intestine 32.2 MB 2,098 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueintestine

Size32.2 MB

Spots2,098

silver H&E NCBI GEO policy

Visium

Mouse intestine

GSM9543400

mouse intestine 29.5 MB 2,307 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueintestine

Size29.5 MB

Spots2,307

silver H&E NCBI GEO policy

Visium

Mouse intestine

GSM9824769

mouse intestine 35.7 MB 2,161 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueintestine

Size35.7 MB

Spots2,161

silver H&E NCBI GEO policy

Cite this collection

No linked publication found — please cite the data source.