Collections / Zika virus co-opts miRNA networks to persist in placental microenvironments detected by spatial transcriptomics [visium]

Zika virus co-opts miRNA networks to persist in placental microenvironments detected by spatial transcriptomics [visium]

Datasets8
Size~1.1 GB
AssayVisium
Samplemouse · multiple
KindComparison
Flag a data issue
10.1016/j.ajog.2023.08.012 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1016-j-ajog-2023-08-012")
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-10.1016/j.ajog.2023.08.012")
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-10-1016-j-ajog-2023-08-012 --dest data/
Install (Python 3.12+) Docs →

Licenses: 8 CC BY-NC-SA 4.0

About the study

Zika virus co-opts microRNA networks to persist in placental niches detected by spatial transcriptomics.

Read the abstract at the source →
Member datasets · 8
Open in Vitessce
Visium
Mouse uterus
NCBI790
mouse uterus 179 MB H&E
TechnologyVisium
Organismmouse
Tissueuterus
Size179 MB
H&E Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
NCBI825
mouse uterus Zika virus infectious disease 93.1 MB 1,159 spots silver H&E
TechnologyVisium
Organismmouse
Tissueuterus
ConditionZika virus infectious disease
Size93.1 MB
Spots1,159
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
NCBI822
mouse uterus Zika virus infectious disease 83.5 MB 706 spots silver H&E
TechnologyVisium
Organismmouse
Tissueuterus
ConditionZika virus infectious disease
Size83.5 MB
Spots706
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
NCBI823
mouse uterus 85.1 MB 875 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueuterus
Size85.1 MB
Spots875
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
NCBI788
mouse uterus Zika virus infectious disease 179 MB 1,182 spots silver H&E
TechnologyVisium
Organismmouse
Tissueuterus
ConditionZika virus infectious disease
Size179 MB
Spots1,182
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse placenta
NCBI791
mouse placenta Zika virus infectious disease 135 MB 429 spots silver H&E
TechnologyVisium
Organismmouse
Tissueplacenta
ConditionZika virus infectious disease
Size135 MB
Spots429
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
NCBI824
mouse uterus Zika virus infectious disease 118 MB 1,709 spots silver H&E
TechnologyVisium
Organismmouse
Tissueuterus
ConditionZika virus infectious disease
Size118 MB
Spots1,709
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
NCBI789
mouse uterus 219 MB 2,302 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueuterus
Size219 MB
Spots2,302
bronze H&E Open in Vitessce

Cite this collection

doi.org/10.1016/j.ajog.2023.08.012 ↗
BibTeX 
@article{Barrozo_2024,
  title = {Zika virus co-opts microRNA networks to persist in placental niches detected by spatial transcriptomics},
  volume = {230},
  ISSN = {0002-9378},
  url = {http://dx.doi.org/10.1016/j.ajog.2023.08.012},
  DOI = {10.1016/j.ajog.2023.08.012},
  number = {2},
  journal = {American Journal of Obstetrics and Gynecology},
  publisher = {Elsevier BV},
  author = {Barrozo, Enrico R. and Seferovic, Maxim D. and Hamilton, Mark P. and Moorshead, David N. and Jochum, Michael D. and Do, Trang and O’Neil, Derek S. and Suter, Melissa A. and Aagaard, Kjersti M.},
  year = {2024},
  month = Feb,
  pages = {251.e1–251.e17}
}