Collections / Spatial transcriptomics on treatment-naïve pancreatic ductal adenocarcinoma (PDAC) patients

Spatial transcriptomics on treatment-naïve pancreatic ductal adenocarcinoma (PDAC) patients

To investigate the spatial distribution of different cell types within the tumor microenvironment in PDAC, we performed Visium spatial transcriptomics (10X Genomics) on FFPE samples from five treatment-naïve PDAC patient tissues.

Datasets5
Size~233 MB
AssayVisium
Samplehuman · pancreas
KindOther
PMID:40154487 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse274103")
coll.ordered_artifacts.df()                 # the 5 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 pancreas
GSM8443450
human pancreas pancreatic ductal adenocarcinoma 57 MB 4,380 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size57 MB
Obs4,380
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8443452
human pancreas pancreatic ductal adenocarcinoma 52 MB 4,983 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size52 MB
Obs4,983
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8443451
human pancreas pancreatic ductal adenocarcinoma 39 MB 4,134 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size39 MB
Obs4,134
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8443453
human pancreas pancreatic ductal adenocarcinoma 46 MB 4,952 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size46 MB
Obs4,952
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM8443449
human pancreas pancreatic ductal adenocarcinoma 39 MB 4,987 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionpancreatic ductal adenocarcinoma
Size39 MB
Obs4,987
silver H&E Open in Vitessce

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