Peripheral afferent neurons terminate at the surfaces of tendons, yet their role after injury beyond nociceptive functions remain unclear. Using transgenic animal models, sensory neurons were found to sprout after Achilles tendon injury in domains of Nerve growth factor (NGF) expression. Conditional deletion of Ngf in either myeloid or mesenchymal cell types led to tendon repair defects – findings phenocopied by inactivation of TrkA (Tropomyosin receptor kinase A) using a knockin mouse model. We sought to identify the signals modulated with neural TrkA inhibition. A combination of single cell and spatial transcriptomic analysis was performed on the Achilles injury site of TrkA^F592A animals and compared them to TrkA^WT.
from sddb import Catalog
cohort = Catalog().collection("geo-gse245097")
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/")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-gse245097")
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()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse245097 --dest data/Licenses: 4 NCBI GEO policy
@article{Cherief_2023,
title = {TrkA-mediated sensory innervation of injured mouse tendon supports tendon sheath progenitor cell expansion and tendon repair},
volume = {15},
ISSN = {1946-6242},
url = {http://dx.doi.org/10.1126/scitranslmed.ade4619},
DOI = {10.1126/scitranslmed.ade4619},
number = {727},
journal = {Science Translational Medicine},
publisher = {American Association for the Advancement of Science (AAAS)},
author = {Cherief, Masnsen and Xu, Jiajia and Li, Zhao and Tower, Robert J. and Ramesh, Sowmya and Qin, Qizhi and Gomez-Salazar, Mario and Yea, Ji-Hye and Lee, Seungyong and Negri, Stefano and Xu, Mingxin and Price, Theodore and Kendal, Adrian R. and Fan, Chen-Ming and Clemens, Thomas L. and Levi, Benjamin and James, Aaron W.},
year = {2023},
month = Dec
}