Collections / Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST]

Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST]

To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and site-matched normal skin

Datasets4
Size~64 MB
AssayVisium
Samplehuman · skin of body
KindReplicates
PMID:32579974 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse144239")
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()}
Open in Vitessce
Visium
Human skin of body
GSM4565825
human skin of body skin squamous cell carcinoma 20 MB 3,650 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditionskin squamous cell carcinoma
Size20 MB
Obs3,650
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM4565826
human skin of body skin squamous cell carcinoma 19 MB 3,838 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditionskin squamous cell carcinoma
Size19 MB
Obs3,838
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM4565824
human skin of body skin squamous cell carcinoma 12 MB 696 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditionskin squamous cell carcinoma
Size12 MB
Obs696
Magnificationother · 3.836 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM4565823
human skin of body skin squamous cell carcinoma 13 MB 744 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditionskin squamous cell carcinoma
Size13 MB
Obs744
Magnificationother · 3.837 µm/px
bronze H&E Open in Vitessce

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