Collections / Mouse uterine gene expressions during peri-implantation period

Mouse uterine gene expressions during peri-implantation period

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

Datasets3
Size~40.4 MB
AssayVisium
Samplemouse · uterus
KindOther
Flag a data issue
PMID:39377223 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse253520")
cohort.members        # the 3 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-gse253520")
coll.ordered_artifacts.to_dataframe()   # the 3 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-gse253520 --dest data/
Install (Python 3.12+) Docs →

Licenses: 3 NCBI GEO policy

Member datasets · 3
Open in Vitessce
Visium
Mouse uterus
GSM8022509
mouse uterus 9.9 MB 296 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueuterus
Size9.9 MB
Spots296
Magnificationother · 3.620 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
GSM8022510
mouse uterus 16.1 MB 502 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueuterus
Size16.1 MB
Spots502
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse uterus
GSM9191330
mouse uterus 14.4 MB 508 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueuterus
Size14.4 MB
Spots508
Magnificationother · 3.621 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1172/jci.insight.181865 ↗
BibTeX 
@article{Aikawa_2024,
  title = {Spatiotemporally distinct roles of cyclooxygenase-1 and cyclooxygenase-2 at fetomaternal interface in mice},
  volume = {9},
  ISSN = {2379-3708},
  url = {http://dx.doi.org/10.1172/jci.insight.181865},
  DOI = {10.1172/jci.insight.181865},
  number = {19},
  journal = {JCI Insight},
  publisher = {American Society for Clinical Investigation},
  author = {Aikawa, Shizu and Matsuo, Mitsunori and Akaeda, Shun and Sugimoto, Yukihiko and Arita, Makoto and Isobe, Yosuke and Sugiura, Yuki and Taira, Shu and Maeda, Rae and Shimizu-Hirota, Ryoko and Takeda, Norihiko and Hiratsuka, Daiki and He, Xueting and Ishizawa, Chihiro and Iida, Rei and Fukui, Yamato and Hiraoka, Takehiro and Harada, Miyuki and Wada-Hiraike, Osamu and Osuga, Yutaka and Hirota, Yasushi},
  year = {2024},
  month = Aug
}