Collections / Spatial transcriptomics of the achilles tendon harvested from the injury site with and without TrkA neuronal inhibition

Spatial transcriptomics of the achilles tendon harvested from the injury site with and without TrkA neuronal inhibition

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.

Datasets4
Size~128 MB
AssayVisium
Samplemouse · calcaneal tendon
KindComparison
PMID:38117901 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse245097")
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
Mouse calcaneal tendon
GSM7836300
mouse calcaneal tendon 33 MB 2,751 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecalcaneal tendon
Size33 MB
Obs2,751
Magnificationother · 14.939 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse calcaneal tendon
GSM7836299
mouse calcaneal tendon 32 MB 2,837 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecalcaneal tendon
Size32 MB
Obs2,837
Magnificationother · 14.876 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse calcaneal tendon
GSM7836297
mouse calcaneal tendon 37 MB 3,047 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecalcaneal tendon
Size37 MB
Obs3,047
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse calcaneal tendon
GSM7836298
mouse calcaneal tendon 26 MB 2,027 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuecalcaneal tendon
Size26 MB
Obs2,027
Magnificationother · 14.891 µm/px
bronze H&E Open in Vitessce

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