Collections / Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences

Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences

Human papillomavirus (HPV) is a major causative factor of head and neck squamous cell carcinoma (HNSCC), and the incidence of HPV-associated HNSCC is increasing. The role of tumor microenvironment (TME) in viral infection and metastasis needs to be explored further. Thus we studied the molecular characteristics of primary tumors (PTs) and lymph node metastatic tumors (LNMTs) by stratifying them based on their HPV status using spatial transcriptomics.

Datasets5
Size~122 MB
AssayVisium
Samplehuman · multiple
KindComparison
PMID:38235919 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse281978")
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()}
Member datasets · 5
Open in Vitessce
Visium
Human lymph node
GSM8633894
human lymph node head and neck squamous cell carcinoma 23 MB 1,908 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditionhead and neck squamous cell carcinoma
Size23 MB
Obs1,908
Magnificationother · 3.270 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human mucosa
GSM8633895
human mucosa head and neck squamous cell carcinoma 19 MB 1,195 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuemucosa
Conditionhead and neck squamous cell carcinoma
Size19 MB
Obs1,195
Magnificationother · 3.273 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human mucosa
GSM8633891
human mucosa head and neck squamous cell carcinoma 26 MB 1,187 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuemucosa
Conditionhead and neck squamous cell carcinoma
Size26 MB
Obs1,187
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8633892
human lymph node head and neck squamous cell carcinoma 35 MB 1,579 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditionhead and neck squamous cell carcinoma
Size35 MB
Obs1,579
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human mucosa
GSM8633893
human mucosa head and neck squamous cell carcinoma 20 MB 1,359 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuemucosa
Conditionhead and neck squamous cell carcinoma
Size20 MB
Obs1,359
bronze H&E Open in Vitessce

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