Collections / Spatial transcriptomic profiling of human saphenous vein grafts reveals molecular remodeling and smooth muscle cell phenotypic transition during early neointima proliferation

Spatial transcriptomic profiling of human saphenous vein grafts reveals molecular remodeling and smooth muscle cell phenotypic transition during early neointima proliferation

Vein graft failure is driven by early neointima l proliferation involving vascular smooth muscle cell (VSMC) proliferation, inflammation, and extracellular matrix remodeling. To elucidate the spatial and transcriptional landscape of this process, we performed spatial transcriptomic profiling of ex vivo cultured human saphenous vein segments at baseline (Day 0) and after 7 days in organ culture. Integration of spatial gene expression with histological features revealed distinct zones of VSMC transdifferentiation, inflammatory activation, and extracellular matrix reorganization. This dataset provides a resource for investigating molecular mechanisms underlying early human vein graft adaptation and neointimal proliferation.

Datasets6
Size~36 MB
AssayVisium
Samplehuman · saphenous vein
KindTime course
PMID:41569144 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse310351")
coll.ordered_artifacts.df()                 # the 6 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
Human saphenous vein
GSM9294395
human saphenous vein 3.8 MB 4,965 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size3.8 MB
Obs4,965
Magnificationother · 3.183 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294393
human saphenous vein 9.1 MB 4,964 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size9.1 MB
Obs4,964
Magnificationother · 3.191 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294396
human saphenous vein 3.8 MB 4,990 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size3.8 MB
Obs4,990
Magnificationother · 3.831 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294397
human saphenous vein 3.9 MB 4,975 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size3.9 MB
Obs4,975
Magnificationother · 3.835 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294398
human saphenous vein 5.8 MB 4,941 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size5.8 MB
Obs4,941
Magnificationother · 3.916 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294394
human saphenous vein 9.4 MB 4,583 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size9.4 MB
Obs4,583
Magnificationother · 3.910 µm/px
bronze H&E Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.