Collections / Eye-conic' spatial transcriptomics of keratoconus corneas

Eye-conic' spatial transcriptomics of keratoconus corneas

The cornea is a transparent, avascular eye tissue composed of five layers: epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium, each of which, if affected by keratoconus (KTCN), may exhibit specific morphological changes. Due to the complexity of the tissue, the studies preserving the spatial location should be applied to identify the layer-specific molecular changes in KTCN, for further understanding of the mechanistic aspects of its cone formation. Study was supported by National Science Centre in Poland, Grant no. 2021/41/B/NZ5/02245 (MG).

Datasets13

Size~130 MB

AssayVisium

Samplehuman · cornea

KindComparison

PMID:41931003 ↗

Download the whole collection

Python · lamindb

import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse303036")
coll.ordered_artifacts.df()                 # the 13 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 · 13

Visium

Human cornea

GSM9116180

human cornea 9.1 MB 1,556 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Size9.1 MB

Obs1,556

Magnificationother · 3.868 µm/px

bronze H&E

Visium

Human cornea

GSM9116170

human cornea keratoconus 11 MB 1,036 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size11 MB

Obs1,036

Magnificationother · 3.813 µm/px

bronze H&E

Visium

Human cornea

GSM9116172

human cornea keratoconus 11 MB 1,065 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size11 MB

Obs1,065

Magnificationother · 3.868 µm/px

bronze H&E

Visium

Human cornea

GSM9116174

human cornea keratoconus 12 MB 1,291 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size12 MB

Obs1,291

Magnificationother · 3.868 µm/px

bronze H&E

Visium

Human cornea

GSM9116175

human cornea keratoconus 9.7 MB 1,646 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size9.7 MB

Obs1,646

Magnificationother · 3.866 µm/px

bronze H&E

Visium

Human cornea

GSM9116176

human cornea 8.9 MB 1,505 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Size8.9 MB

Obs1,505

Magnificationother · 3.868 µm/px

bronze H&E

Visium

Human cornea

GSM9116171

human cornea keratoconus 10 MB 1,575 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size10 MB

Obs1,575

Magnificationother · 3.866 µm/px

bronze H&E

Visium

Human cornea

GSM9116178

human cornea 9.6 MB 1,727 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Size9.6 MB

Obs1,727

bronze H&E

Visium

Human cornea

GSM9116173

human cornea keratoconus 9.8 MB 1,226 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size9.8 MB

Obs1,226

bronze H&E

Visium

Human cornea

GSM9116177

human cornea 11 MB 2,357 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Size11 MB

Obs2,357

bronze H&E

Visium

Human cornea

GSM9116169

human cornea keratoconus 9.4 MB 950 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size9.4 MB

Obs950

bronze H&E

Visium

Human cornea

GSM9116181

human cornea keratoconus 8.9 MB 1,368 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Conditionkeratoconus

Size8.9 MB

Obs1,368

bronze H&E

Visium

Human cornea

GSM9116179

human cornea 10 MB 1,886 obs bronze H&E

TechnologyVisium

Organismhuman

Tissuecornea

Size10 MB

Obs1,886

Magnificationother · 3.866 µm/px

bronze H&E

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