Collections / Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Spatial Transcriptomics]

Multi-omics analysis identifies erythroid cells as the major population in mouse placentas expressing the MHC class II antigen presentation, chemokine, and antibacterial immune response genes [Spatial Transcriptomics]

Pregnancy is one of the most important processes for mammals, which is deeply controlled by the immune system. We performed spatial transcriptomics to profile mouse placentas from semi-allogeneic and syngeneic pregnancies at E12.5 to elucidate differences between these types of pregnancies. Our analysis showed that erythroid cells were the major immunoregulatory population in both types of pregnancies.

Datasets3
Size~97.8 MB
AssayVisium
Samplemouse · placenta
KindOther
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PMID:41058694 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse289170")
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-gse289170")
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-gse289170 --dest data/
Install (Python 3.12+) Docs →

Licenses: 3 NCBI GEO policy

Member datasets · 3
Open in Vitessce
Visium
Mouse placenta
GSM8785671
mouse placenta 35.2 MB 2,898 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueplacenta
Size35.2 MB
Spots2,898
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse placenta
GSM8785670
mouse placenta 32.1 MB 3,569 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueplacenta
Size32.1 MB
Spots3,569
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse placenta
GSM8785666
mouse placenta 30.5 MB 2,599 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueplacenta
Size30.5 MB
Spots2,599
silver H&E NCBI GEO policy Open in Vitessce

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No linked publication found — please cite the data source.