Collections / Time-series spatial transcriptomic analysis of murine colon undergoing AOM-DSS tumorigenesis with and without LXR activation

Time-series spatial transcriptomic analysis of murine colon undergoing AOM-DSS tumorigenesis with and without LXR activation

To unbiasedly characterize the spatial transcriptomics landscape of murine colorectal cancer initiation and progression, we performed a time-series spatial transcriptional analysis of total colonic tissue during the course of azoxymethane (AOM)-dextran sodium sulfate (DSS) induced colorectal cancer from mice receiving standard (chow) diet. Additionally, to understand the role of LXR activation during AOM-DSS tumorigenesis, we also collected colonic tissues from mice fed with GW3965 diet.

Datasets5
Size~262 MB
AssayVisium
Samplemouse · colon
KindTime course
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PMID:39567700 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse227598")
cohort.members        # the 5 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-gse227598")
coll.ordered_artifacts.to_dataframe()   # the 5 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-gse227598 --dest data/
Install (Python 3.12+) Docs →

Licenses: 5 NCBI GEO policy

Member datasets · 5
Open in Vitessce
Visium
Mouse colon
GSM7103783
mouse colon colorectal cancer 50.1 MB 3,471 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size50.1 MB
Spots3,471
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103784
mouse colon colorectal cancer 49.7 MB 4,291 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size49.7 MB
Spots4,291
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103781
mouse colon colorectal cancer 58.7 MB 4,585 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size58.7 MB
Spots4,585
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103780
mouse colon 44.4 MB 3,052 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecolon
Size44.4 MB
Spots3,052
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103782
mouse colon colorectal cancer 59.5 MB 4,344 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size59.5 MB
Spots4,344
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.