Classic galactosemia (CG) is a rare inborn error of galactose metabolism caused by mutations in GALT gene. Primary ovarian insufficiency (POI) is a later complication that affects 80% of women with CG due to significant decline in ovarian follicle reserve. The definite mechanisms underlying the early onset of POI in CG patients is not fully understood. We utilized spatial transcriptomics from 10x Visium to generate spatial landscape of human ovaries from pre-pubertal girls with CG to investigate dynamic gene expression profiles in the ovarian follicles and stromal cells.
from sddb import Catalog
cohort = Catalog().collection("geo-gse268523")
cohort.members # the 6 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/")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-gse268523")
coll.ordered_artifacts.to_dataframe() # the 6 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse268523 --dest data/Licenses: 6 NCBI GEO policy
@article{Kavarthapu_2024,
title = {Single‐nucleus and spatial transcriptomics of paediatric ovary: Molecular insights into the dysregulated signalling pathways underlying premature ovarian insufficiency in classic galactosemia},
volume = {14},
ISSN = {2001-1326},
url = {http://dx.doi.org/10.1002/ctm2.70043},
DOI = {10.1002/ctm2.70043},
number = {10},
journal = {Clinical and Translational Medicine},
publisher = {Wiley},
author = {Kavarthapu, Raghuveer and Lou, Hong and Pham, Thang and Do, Han and Soliman, Mary E. and Badger, Taylor and Balasubramanian, Ramya and Huyhn, Victoria and De La Luz Sierra, Maria and Yano Maher, Jacqueline C. and Gomez‐Lobo, Veronica},
year = {2024},
month = Oct
}