Collections / Spatial gene expression and microenvironmental changes in the transition of nevus to melanoma

Spatial gene expression and microenvironmental changes in the transition of nevus to melanoma

Approximately one-third of melanomas arise from benign nevi, yet the transcriptional and microenvironmental changes accompanying this transition remain incompletely understood. To study the nevus-to-melanoma transition, we employed genome-wide spatial transcriptomics combined with imaging mass cytometry on adjacent nevus-melanoma lesions.

Datasets11
Size~692 MB
AssayVisium
Samplehuman · skin of body
KindReplicates
PMID:42258703 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse298774")
coll.ordered_artifacts.df()                 # the 11 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 · 11
Open in Vitessce
Visium
Human skin of body
GSM9022963
human skin of body cutaneous melanoma 22 MB 13,887 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size22 MB
Obs13,887
Magnificationother · 10.181 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022964
human skin of body cutaneous melanoma 22 MB 4,985 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size22 MB
Obs4,985
Magnificationother · 4.021 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022971
human skin of body cutaneous melanoma 25 MB 14,210 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size25 MB
Obs14,210
Magnificationother · 8.062 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022969
human skin of body cutaneous melanoma 161 MB 14,328 obs bronze
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size161 MB
Obs14,328
bronze Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022966
human skin of body cutaneous melanoma 46 MB 5,195 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size46 MB
Obs5,195
Magnificationother · 10.780 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022965
human skin of body cutaneous melanoma 28 MB 2,260 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size28 MB
Obs2,260
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022973
human skin of body cutaneous melanoma 44 MB 4,991 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size44 MB
Obs4,991
Magnificationother · 5.510 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022970
human skin of body cutaneous melanoma 104 MB 14,331 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size104 MB
Obs14,331
Magnificationother · 8.321 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022972
human skin of body cutaneous melanoma 27 MB 14,145 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size27 MB
Obs14,145
Magnificationother · 7.873 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022967
human skin of body cutaneous melanoma 194 MB 14,336 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size194 MB
Obs14,336
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human skin of body
GSM9022968
human skin of body cutaneous melanoma 20 MB 14,203 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueskin of body
Conditioncutaneous melanoma
Size20 MB
Obs14,203
Magnificationother · 8.164 µm/px
bronze H&E Open in Vitessce

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