Collections / Spatial Multi-omics Reveals the Heterogeneity of Tumor Microenvironment in the OSF-Associated OSCC

Spatial Multi-omics Reveals the Heterogeneity of Tumor Microenvironment in the OSF-Associated OSCC

Oral submucous fibrosis (OSF) is one of the most common precancerous malignant orders (PMO) with high rates exacerbating into oral squamous cell carcinoma (OSCC), mostly occurred in patients with chewing betel-nut habits in Southeast Asia and Pacific region. However, the spatial characteristics and heteogeneities of tumor microenvironment (TME) in OSF-associated OSCC still remains unclear. Here, we characterized the spatiotemporal changes of OSF-associated OSCC at different malignant states by performing 10x Visium Spatial Transcriptomics (ST) sequencing and airflow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) analysis.

Datasets4
Size~215 MB
AssayVisium
Samplehuman · mouth
KindReplicates
PMID:38229179 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse220978")
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()}
Member datasets · 4
Open in Vitessce
Visium
Human mouth
GSM6833487
human mouth oral cavity squamous cell carcinoma 54 MB 4,316 obs silver H&E
TechnologyVisium
Organismhuman
Tissuemouth
Conditionoral cavity squamous cell carcinoma
Size54 MB
Obs4,316
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human mouth
GSM6833484
human mouth oral cavity squamous cell carcinoma 63 MB 4,199 obs silver H&E
TechnologyVisium
Organismhuman
Tissuemouth
Conditionoral cavity squamous cell carcinoma
Size63 MB
Obs4,199
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human mouth
GSM6833486
human mouth oral cavity squamous cell carcinoma 44 MB 4,514 obs silver H&E
TechnologyVisium
Organismhuman
Tissuemouth
Conditionoral cavity squamous cell carcinoma
Size44 MB
Obs4,514
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human mouth
GSM6833485
human mouth oral cavity squamous cell carcinoma 54 MB 4,290 obs silver H&E
TechnologyVisium
Organismhuman
Tissuemouth
Conditionoral cavity squamous cell carcinoma
Size54 MB
Obs4,290
silver H&E Open in Vitessce

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