Collections / Spatial Transcriptomics of Brains Infected with VEEV

Spatial Transcriptomics of Brains Infected with VEEV

Venezuelan equine encephalitis virus (VEEV) is a neurotropic alphavirus that causes neurological disease in both humans and equine. In this study we paired spatial transcriptomics and a mouse model of VEEV to generate a transcriptomic profile of infected or control brains at 6 days post infection. We identified regionally distinct myeloid and lymphocyte populations, contributing to our understanding of the neuroinflammation caused by VEEV.

Datasets2
Size~122 MB
AssayVisium
Samplemouse · brain
KindTime course
PMID:39749347 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse275201")
coll.ordered_artifacts.df()                 # the 2 members, ordered

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

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Member datasets · 2
Open in Vitessce
Visium
Mouse brain
GSM8472671
mouse brain 72 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size72 MB
Obs4,992
Magnificationother · 5.453 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8472672
mouse brain Venezuelan equine encephalitis 49 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuebrain
ConditionVenezuelan equine encephalitis
Size49 MB
Obs4,992
Magnificationother · 5.488 µm/px
bronze H&E Open in Vitessce

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