Collections / Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -Spatial Transcriptomics

Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -Spatial Transcriptomics

ADAR1 is thought to be an immune suppressor maintaining self-tolerance to endogenous nucleic acids. Lack of ADAR1 results in MDA5 (Ifih1) activation and MDA5 deletion rescues ADAR1 null embryonic lethality. We generated liver specific ADAR1; MDA5 double KO mice and performed high throughput sequencing to investigate hepatic inflammation in these mice. Spatial transcriptomics (Visium, 10x Genomics) was performed on FFPE mice liver tissues. Constructed libraries were sequenced on the Novaseq 6000 platform. Over 250 million pairs of mappable reads for each sample were obtained.

Datasets9
Size~353 MB
AssayVisium
Samplemouse · liver
KindComparison
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PMID:38935501 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse228195")
cohort.members        # the 9 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-gse228195")
coll.ordered_artifacts.to_dataframe()   # the 9 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-gse228195 --dest data/
Install (Python 3.12+) Docs →

Licenses: 9 NCBI GEO policy

Member datasets · 9
Open in Vitessce
Visium
Mouse liver
GSM7116322
mouse liver 55.4 MB 4,538 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size55.4 MB
Spots4,538
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116328
mouse liver 31.2 MB 2,736 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size31.2 MB
Spots2,736
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116324
mouse liver 33.5 MB 2,737 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size33.5 MB
Spots2,737
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116326
mouse liver 32.4 MB 2,868 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size32.4 MB
Spots2,868
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116329
mouse liver 33.7 MB 2,741 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size33.7 MB
Spots2,741
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116325
mouse liver 33.7 MB 2,928 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size33.7 MB
Spots2,928
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116323
mouse liver 45.5 MB 4,579 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size45.5 MB
Spots4,579
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116327
mouse liver 34.9 MB 2,868 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size34.9 MB
Spots2,868
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116321
mouse liver 52.7 MB 4,198 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size52.7 MB
Spots4,198
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.