Collections / Spatial characterization of the transcriptome of the adult healthy and mutant FUS mouse spinal cords [Spatial transcriptomics]

Spatial characterization of the transcriptome of the adult healthy and mutant FUS mouse spinal cords [Spatial transcriptomics]

Here we investigated the spatial transcriptome of the aged mouse spinal cord using 10X Genomics Visium platform. We produced local transcriptomes of the full spinal cord with a resolution of 100 um, characterizing ventral and dorsal horn regions, in addition to grey and white matter regions. With these spatial data, it is possible to explore the spatial transcriptome of the aged mouse spinal cord, extrapolating information on the cellular composition of this tissue.

Datasets4
Size~47.6 MB
AssayVisium
Samplemouse · spinal cord
KindOther
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PMID:41430470 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse269377")
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-gse269377")
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-gse269377 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Visium
Mouse spinal cord
GSM8314106
mouse spinal cord 11.8 MB 4,992 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size11.8 MB
Spots4,992
Magnificationother · 4.059 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8314109
mouse spinal cord 11.2 MB 4,992 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size11.2 MB
Spots4,992
Magnificationother · 4.059 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8314108
mouse spinal cord 9.9 MB 4,992 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size9.9 MB
Spots4,992
Magnificationother · 4.057 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8314107
mouse spinal cord 14.6 MB 4,992 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size14.6 MB
Spots4,992
Magnificationother · 4.060 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1038/s41593-025-02101-2 ↗
BibTeX 
@article{Piol_2025,
  title = {Axonal Eif5a hypusination controls local translation and mitigates defects in FUS-ALS},
  volume = {29},
  ISSN = {1546-1726},
  url = {http://dx.doi.org/10.1038/s41593-025-02101-2},
  DOI = {10.1038/s41593-025-02101-2},
  number = {1},
  journal = {Nature Neuroscience},
  publisher = {Springer Science and Business Media LLC},
  author = {Piol, Diana and Khalil, Bilal and Robberechts, Tessa and Killian, Theo and Georgopoulou, Maria and Partel, Gabriele and Wouters, David and Hecker, Nikolai and Tziortzouda, Paraskevi and Verresen, Yana and Corthout, Nikky and Kint, Sam and Vandereyken, Katy and Van Damme, Philip and Voet, Thierry and Davie, Kristofer and Poovathingal, Suresh and Van Den Bosch, Ludo and Aerts, Stein and Sifrim, Alejandro and Da Cruz, Sandrine},
  year = {2025},
  month = Dec,
  pages = {53–66}
}