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~128 MB
AssayVisium
Samplemouse · brain
KindTime course
Flag a data issue
PMID:39749347 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse275201")
cohort.members        # the 2 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-gse275201")
coll.ordered_artifacts.to_dataframe()   # the 2 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-gse275201 --dest data/
Install (Python 3.12+) Docs →

Licenses: 2 NCBI GEO policy

Member datasets · 2
Open in Vitessce
Visium
Mouse brain
GSM8472671
mouse brain 75.8 MB 4,992 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size75.8 MB
Spots4,992
Magnificationother · 5.453 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8472672
mouse brain Venezuelan equine encephalitis 51.7 MB 4,992 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
ConditionVenezuelan equine encephalitis
Size51.7 MB
Spots4,992
Magnificationother · 5.488 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.3389/fimmu.2024.1497839 ↗
BibTeX 
@article{Rangel_2024,
  title = {Single-cell and spatiotemporal transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection},
  volume = {15},
  ISSN = {1664-3224},
  url = {http://dx.doi.org/10.3389/fimmu.2024.1497839},
  DOI = {10.3389/fimmu.2024.1497839},
  journal = {Frontiers in Immunology},
  publisher = {Frontiers Media SA},
  author = {Rangel, Margarita V. and Sebastian, Aimy and Leon, Nicole F. and Phillips, Ashlee M. and Gorman, Bria M. and Hum, Nicholas R. and Weilhammer, Dina R.},
  year = {2024},
  month = Dec
}