Mouse liver
GSM8285400
mouse liver malaria 21.3 MB 2,693 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionmalaria
Spots2,693
Magnificationother · 3.503 µm/px
bronze H&E NCBI GEO policy
Collections / Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution (VISIUM)
Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution (VISIUM)
During liver infection, the malaria parasite undergoes massive replication whilst remaining clinically silent. Spatial coordination of immune response regulation and metabolic zonation during malaria infection in the true tissue context remains unexplored. We perform spatial transcriptomics combined with snRNA-seq over multiple time points to delineate transcriptional programs of host-pathogen interactions across P. berghei-infected liver tissues. Our data suggest changes in gene expression related to lipid metabolism adjacent to infected hepatocytes, particularly modulation of the expression of genes involved in peroxisome proliferator-activated receptor pathway signaling. The data further indicates the presence of inflammatory hotspots with differential inflammation programs along the lobular axis in infected tissues. Additionally, upregulation of genes involved in inflammation is observed, but considerably delayed, in livers of control mice injected with mosquito salivary gland components. Our study establishes a benchmark for investigating host-parasite interactions, and can easily be implemented to validate de novo malaria drug and vaccine efforts.
Datasets4
Size~104 MB
AssayVisium
Samplemouse · liver
KindTime course
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse268068")
cohort.members # the 4 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/") 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-gse268068")
coll.ordered_artifacts.to_dataframe() # the 4 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse268068 --dest data/Licenses: 4 NCBI GEO policy
Member datasets · 4
Mouse liver
GSM8285399
mouse liver malaria 26.3 MB 2,902 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionmalaria
Spots2,902
Magnificationother · 3.503 µm/px
bronze H&E NCBI GEO policy
Mouse liver
GSM8285402
mouse liver malaria 26.8 MB 2,676 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionmalaria
Spots2,676
Magnificationother · 3.502 µm/px
bronze H&E NCBI GEO policy
Mouse liver
GSM8285401
mouse liver malaria 30.1 MB 2,999 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionmalaria
Spots2,999
Magnificationother · 3.503 µm/px
bronze H&E NCBI GEO policy
Cite this collection
doi.org/10.1038/s41467-024-51418-2 ↗ BibTeX
@article{Hildebrandt_2024,
title = {Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution},
volume = {15},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-024-51418-2},
DOI = {10.1038/s41467-024-51418-2},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Hildebrandt, Franziska and Iturritza, Miren Urrutia and Zwicker, Christian and Vanneste, Bavo and Van Hul, Noémi and Semle, Elisa and Quin, Jaclyn and Pascini, Tales and Saarenpää, Sami and He, Mengxiao and Andersson, Emma R. and Scott, Charlotte L. and Vega-Rodriguez, Joel and Lundeberg, Joakim and Ankarklev, Johan},
year = {2024},
month = Aug
}