Collections / spatialRNAseq_heart_raw_suppdata

spatialRNAseq_heart_raw_suppdata

Datasets8
Size~4.9 GB
AssayVisium
Samplemouse · multiple
KindComparison
Flag a data issue
10.1038/s44161-022-00138-1 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1038-s44161-022-00138-1")
cohort.members        # the 8 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="doi-10.1038/s44161-022-00138-1")
coll.ordered_artifacts.to_dataframe()   # the 8 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 doi-10-1038-s44161-022-00138-1 --dest data/
Install (Python 3.12+) Docs →

Licenses: 8 CC BY-NC-SA 4.0

About the study

Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.

A significant fraction of sudden death in children and young adults is due to viral myocarditis, an inflammatory disease of the heart. In this study, by using integrated single-cell and spatial transcriptomics, we created a high-resolution, spatially resolved transcriptome map of reovirus-induced myocarditis in neonatal mouse hearts. We assayed hearts collected at three timepoints after infection and studied the temporal, spatial and cellular heterogeneity of host-virus interactions. We further assayed the intestine, the primary site of reovirus infection, to establish a full chronology of molecular events that ultimately lead to myocarditis. We found that inflamed endothelial cells recruit cytotoxic T cells and undergo pyroptosis in the myocarditic tissue. Analyses of spatially restricted gene expression in myocarditic regions and the border zone identified immune-mediated cell-type-specific injury and stress responses. Overall, we observed a complex network of cellular phenotypes and spatially restricted cell-cell interactions associated with reovirus-induced myocarditis in neonatal mice.

Member datasets · 8
Open in Vitessce
Visium
Mouse intestine
MEND32
mouse intestine 579 MB 1,970 spots silver H&E
TechnologyVisium
Organismmouse
Tissueintestine
Size579 MB
Spots1,970
Magnification20x · 0.360 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse intestine
MEND29
mouse intestine 686 MB 2,161 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueintestine
Size686 MB
Spots2,161
Magnification20x · 0.360 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse intestine
MEND31
mouse intestine 714 MB 2,152 spots silver H&E
TechnologyVisium
Organismmouse
Tissueintestine
Size714 MB
Spots2,152
Magnification20x · 0.360 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
MEND28
mouse heart 500 MB 1,835 spots silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Size500 MB
Spots1,835
Magnification20x · 0.360 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
MEND26
mouse heart viral myocarditis 430 MB 1,372 spots silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionviral myocarditis
Size430 MB
Spots1,372
Magnification20x · 0.360 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse intestine
MEND30
mouse intestine 613 MB 1,744 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueintestine
Size613 MB
Spots1,744
Magnification20x · 0.361 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
MEND25
mouse heart viral myocarditis 632 MB 2,278 spots silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionviral myocarditis
Size632 MB
Spots2,278
Magnification20x · 0.360 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
MEND27
mouse heart 710 MB 2,758 spots silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Size710 MB
Spots2,758
Magnification20x · 0.360 µm/px
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1038/s44161-022-00138-1 ↗
BibTeX 
@article{Mantri_2022,
  title = {Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis},
  volume = {1},
  ISSN = {2731-0590},
  url = {http://dx.doi.org/10.1038/s44161-022-00138-1},
  DOI = {10.1038/s44161-022-00138-1},
  number = {10},
  journal = {Nature Cardiovascular Research},
  publisher = {Springer Science and Business Media LLC},
  author = {Mantri, Madhav and Hinchman, Meleana M. and McKellar, David W. and Wang, Michael F. Z. and Cross, Shaun T. and Parker, John S. L. and De Vlaminck, Iwijn},
  year = {2022},
  month = Oct,
  pages = {946–960}
}