Collections / Spatial transcriptomic landscape of protein-coding genes in descended and undescended testes of dogs with unilateral cryptorchidism

Spatial transcriptomic landscape of protein-coding genes in descended and undescended testes of dogs with unilateral cryptorchidism

Cryptorchidism is a common congenital disorder of the male reproductive system in dogs. We used the 10x Genomics Visium Spatial Gene Expression platform to profile four testicular tissue sections from two dogs with unilateral cryptorchidism: an abdominally retained testis and its contralateral descended testis, and an inguinally retained testis and its contralateral descended testis. The data reveal spot-level transcriptional differences, depletion of germ cell-associated signatures, and enrichment of Sertoli and peritubular myoid cell-associated signals in the retained testes. Because only two dogs were studied, differential-expression results are descriptive and hypothesis-generating.

Datasets4
Size~203 MB
AssayVisium
Sampledog · testis
KindComparison
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www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE344594 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse344594")
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-gse344594")
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-gse344594 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Visium
Dog testis
GSM9982019
dog testis cryptorchidism 36.6 MB 4,136 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismdog
Tissuetestis
Conditioncryptorchidism
Size36.6 MB
Spots4,136
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Dog testis
GSM9982018
dog testis 56.4 MB 4,731 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismdog
Tissuetestis
Size56.4 MB
Spots4,731
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Dog testis
GSM9982017
dog testis cryptorchidism 51.6 MB 3,929 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismdog
Tissuetestis
Conditioncryptorchidism
Size51.6 MB
Spots3,929
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Dog testis
GSM9982020
dog testis 57.9 MB 4,273 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismdog
Tissuetestis
Size57.9 MB
Spots4,273
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.