Collections / Spatial transcriptomic analysis of a pre-clinical NF1 pseudarthrosis fracture model

Spatial transcriptomic analysis of a pre-clinical NF1 pseudarthrosis fracture model

Patients with Neurofibromatosis Type 1 (NF1) present with fracture pseudarthroses, though the exact mechanism underlying this abnormal healing remains unknown. Here, we performed spatial transcriptomics to spatially-define the molecular signatures across endochondral healing following fracture. Integrating single-cell sequencing of patient fracture-derived primary cells, our results provide a dynamic cellular context to the molecular dysregulation associated with somatic fracture healing defects in NF1.

Datasets2
Size~66.3 MB
AssayVisium
Samplemouse · tibia
KindOther
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PMID:38990653 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse218046")
cohort.members        # the 2 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-gse218046")
coll.ordered_artifacts.to_dataframe()   # the 2 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-gse218046 --dest data/
Install (Python 3.12+) Docs →

Licenses: 2 NCBI GEO policy

Member datasets · 2
Open in Vitessce
Visium
Mouse tibia
GSM6733377
mouse tibia 32.0 MB 3,045 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuetibia
Size32.0 MB
Spots3,045
Magnificationother · 3.704 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse tibia
GSM6733378
mouse tibia 34.3 MB 3,335 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuetibia
Size34.3 MB
Spots3,335
Magnificationother · 3.641 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1172/jci.insight.176802 ↗
BibTeX 
@article{Rios_2024,
  title = {Spatial transcriptomics implicates impaired BMP signaling in NF1 fracture pseudarthrosis in murine and patient tissues},
  volume = {9},
  ISSN = {2379-3708},
  url = {http://dx.doi.org/10.1172/jci.insight.176802},
  DOI = {10.1172/jci.insight.176802},
  number = {16},
  journal = {JCI Insight},
  publisher = {American Society for Clinical Investigation},
  author = {Rios, Jonathan J. and Juan, Conan and Shelton, John M. and Paria, Nandina and Oxendine, Ila and Wassell, Meghan and Kidane, Yared H. and Cornelia, Reuel and Jeffery, Elise C. and Podeszwa, David A. and Conway, Simon J. and Wise, Carol A. and Tower, Robert J.},
  year = {2024},
  month = July
}