Collections / Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair.

Spatially-restricted and ontogenically-distinct hepatic macrophages are required for tissue repair.

Analysis of single cell RNA-seq, CITE-seq data and bulk RNA-seq data on cells isolated from the livers of mice following PBS and APAP (paracetamol/acetaminophen) administration. Spatial Transcriptomics analysis was performed using 10x Visium platform on mouse livers 48hrs post PBS or APAP administration. We also analysed single cell RNA-seq data on CD64+F4/80+ macrophages isolated from the livers of Trem2 fl/fl mice and CD64CRE Trem2 fl/fl mice.

Datasets3

Size~57.9 MB

AssayVisium

Samplemouse · liver

KindComparison

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PMID:39862865 ↗

Download the whole collection

Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse280515")
cohort.members        # the 3 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-gse280515")
coll.ordered_artifacts.to_dataframe()   # the 3 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-gse280515 --dest data/

Install (Python 3.12+) Docs →

Licenses: 3 NCBI GEO policy

Member datasets · 3

Visium

Mouse liver

GSM8599604

mouse liver drug-induced liver injury 25.4 MB 2,178 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditiondrug-induced liver injury

Size25.4 MB

Spots2,178

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM8599603

mouse liver drug-induced liver injury 17.3 MB 1,272 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Conditiondrug-induced liver injury

Size17.3 MB

Spots1,272

silver H&E NCBI GEO policy

Visium

Mouse liver

GSM8599602

mouse liver 15.3 MB 1,790 spots silver H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissueliver

Size15.3 MB

Spots1,790

silver H&E NCBI GEO policy

Cite this collection

No linked publication found — please cite the data source.