Collections / Integrative single-cell transcriptome analysis of human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis [Spatial]

Integrative single-cell transcriptome analysis of human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis [Spatial]

We identified five distinct functional subclusters of pancreatic cancer cells and six distinct cancer-associated fibroblast subclusters. We deeply profiled their characteristics, and we found that these subclusters successfully deconvoluted most of the features suggested in bulk transcriptome analysis of pancreatic cancer. Among those subclusters, we identified a novel cancer cell subcluster, Ep_VGLL1, showing intermediate characteristics between the extremities of basal-like and classical dichotomy, despite its prognostic value. Molecular features of Ep_VGLL1 suggest its transitional properties between basal-like and classical subtypes, which is strongly supported by spatial transcriptome data.

Datasets7
Size~281 MB
AssayVisium
Samplehuman · pancreas
KindOther
PMID:38297291 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse235315")
coll.ordered_artifacts.df()                 # the 7 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()}
Member datasets · 7
Open in Vitessce
Visium
Human pancreas
GSM7498815
human pancreas exocrine pancreatic carcinoma 32 MB 3,168 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionexocrine pancreatic carcinoma
Size32 MB
Obs3,168
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM7498813
human pancreas exocrine pancreatic carcinoma 53 MB 4,373 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionexocrine pancreatic carcinoma
Size53 MB
Obs4,373
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM7498816
human pancreas exocrine pancreatic carcinoma 42 MB 3,582 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionexocrine pancreatic carcinoma
Size42 MB
Obs3,582
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM7498814
human pancreas exocrine pancreatic carcinoma 42 MB 4,649 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionexocrine pancreatic carcinoma
Size42 MB
Obs4,649
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM7498812
human pancreas exocrine pancreatic carcinoma 24 MB 2,248 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionexocrine pancreatic carcinoma
Size24 MB
Obs2,248
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM7498811
human pancreas exocrine pancreatic carcinoma 60 MB 3,947 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionexocrine pancreatic carcinoma
Size60 MB
Obs3,947
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pancreas
GSM7498817
human pancreas exocrine pancreatic carcinoma 28 MB 3,468 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepancreas
Conditionexocrine pancreatic carcinoma
Size28 MB
Obs3,468
silver H&E Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.