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~193 MB
AssayVisium
Sampledog · testis
KindComparison
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE344594 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse344594")
coll.ordered_artifacts.df()                 # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Open in Vitessce
Visium
Dog testis
GSM9982019
dog testis cryptorchidism 35 MB 4,136 obs silver H&E
TechnologyVisium
Organismdog
Tissuetestis
Conditioncryptorchidism
Size35 MB
Obs4,136
silver H&E Open in Vitessce
Open in Vitessce
Visium
Dog testis
GSM9982018
dog testis 54 MB 4,731 obs silver H&E
TechnologyVisium
Organismdog
Tissuetestis
Size54 MB
Obs4,731
silver H&E Open in Vitessce
Open in Vitessce
Visium
Dog testis
GSM9982017
dog testis cryptorchidism 49 MB 3,929 obs silver H&E
TechnologyVisium
Organismdog
Tissuetestis
Conditioncryptorchidism
Size49 MB
Obs3,929
silver H&E Open in Vitessce
Open in Vitessce
Visium
Dog testis
GSM9982020
dog testis 55 MB 4,273 obs silver H&E
TechnologyVisium
Organismdog
Tissuetestis
Size55 MB
Obs4,273
silver H&E Open in Vitessce

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