Collections / Mouse uterine gene expressions during decidual processes [Visium]

Mouse uterine gene expressions during decidual processes [Visium]

Spatiotemporal uterine gene expressions during peri-implantation period at pregnancy day 4 and 6 was investigated by scRNA-seq and Visium spatial transcriptome.

Datasets4
Size~89.1 MB
AssayVisium
Samplemouse · uterus
KindComparison
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PMID:42154563 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse296581")
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/")
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-gse296581")
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()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse296581 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Visium
Mouse uterus
GSM8972900
mouse uterus 14.3 MB 478 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueuterus
Size14.3 MB
Spots478
Magnificationother · 3.622 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
GSM8972901
mouse uterus 22.4 MB 946 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueuterus
Size22.4 MB
Spots946
Magnificationother · 3.621 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
GSM8972902
mouse uterus 20.8 MB 854 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueuterus
Size20.8 MB
Spots854
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
GSM8972899
mouse uterus 31.6 MB 1,530 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueuterus
Size31.6 MB
Spots1,530
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1073/pnas.2528309123 ↗
BibTeX 
@article{He_2026,
  title = {TAZ integrates ECM remodeling with uterine stromal differentiation to maintain early pregnancy},
  volume = {123},
  ISSN = {1091-6490},
  url = {http://dx.doi.org/10.1073/pnas.2528309123},
  DOI = {10.1073/pnas.2528309123},
  number = {21},
  journal = {Proceedings of the National Academy of Sciences},
  publisher = {National Academy of Sciences},
  author = {He, Xueting and Aikawa, Shizu and Fukui, Yamato and Ishizawa, Chihiro and Shimizu-Hirota, Ryoko and Hiratsuka, Daiki and Hiraoka, Takehiro and Matsuo, Mitsunori and Hirota, Yasushi},
  year = {2026},
  month = May
}