Collections / Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [Xenium]

Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [Xenium]

Skin injuries heal slowly, compared to oral epithelial tissues, and often do not regenerate lost adnexa. Using a murine mouse model expressing the oral epithelial transcription factor PITX1 in the skin, we performed Xenium in situ analysis in healthy and wounded skin and healthy oral mucosa to delineate the cellular and molecular changes underpinning the superior oral wounding response.

Datasets4
Size~2.3 GB
Assay10x Xenium
Samplemouse · multiple
KindComparison
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PMID:39480496 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse280069")
cohort.members        # the 4 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
Install (Python 3.12+) Docs →
Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse280069")
coll.ordered_artifacts.to_dataframe()   # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse280069 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
10x Xenium
Mouse skin of back
GSM8586920
mouse skin of back 419 MB 91,345 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissueskin of back
Size419 MB
Cells91,345
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse skin of back
GSM8586921
mouse skin of back 673 MB 182,402 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissueskin of back
Size673 MB
Cells182,402
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse skin of back
GSM8586923
mouse skin of back 704 MB 174,241 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissueskin of back
Size704 MB
Cells174,241
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse buccal mucosa
GSM8586922
mouse buccal mucosa 548 MB 67,803 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebuccal mucosa
Size548 MB
Cells67,803
bronze NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.