Collections / Spatial transcriptomics of the ageing ovary

Spatial transcriptomics of the ageing ovary

Ageing is a physiological process that manifests through progressive molecular, cellular, and systemic changes. Female reproductive potential gradually declines with age as oocyte quality and quantity decline. The purpose of this study was to better understand the spatiotemporal dynamics of the ovary.

Datasets4
Size~76.9 MB
AssayVisium
Samplemouse · ovary
KindOther
Flag a data issue
PMID:35996587 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse188257")
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-gse188257")
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-gse188257 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Visium
Mouse ovary
GSM5673399
mouse ovary 25.3 MB 1,415 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueovary
Size25.3 MB
Spots1,415
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse ovary
GSM5673400
mouse ovary 13.9 MB 814 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueovary
Size13.9 MB
Spots814
Magnificationother · 11.498 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse ovary
GSM5673398
mouse ovary 15.7 MB 841 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueovary
Size15.7 MB
Spots841
Magnificationother · 11.192 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse ovary
GSM5673401
mouse ovary 22.1 MB 1,193 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueovary
Size22.1 MB
Spots1,193
Magnificationother · 11.114 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1016/j.isci.2022.104819 ↗
BibTeX 
@article{Russ_2022,
  title = {Spatially resolved transcriptomic profiling of ovarian aging in mice},
  volume = {25},
  ISSN = {2589-0042},
  url = {http://dx.doi.org/10.1016/j.isci.2022.104819},
  DOI = {10.1016/j.isci.2022.104819},
  number = {8},
  journal = {iScience},
  publisher = {Elsevier BV},
  author = {Russ, Jennifer E. and Haywood, Mary E. and Lane, Sydney L. and Schoolcraft, William B. and Katz-Jaffe, Mandy G.},
  year = {2022},
  month = Aug,
  pages = {104819}
}