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~250 MB
AssayVisium
Samplemouse · colon
KindTime course
PMID:39567700 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse227598")
coll.ordered_artifacts.df()                 # the 5 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 · 5
Open in Vitessce
Visium
Mouse colon
GSM7103783
mouse colon colorectal cancer 48 MB 3,471 obs silver H&E
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size48 MB
Obs3,471
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103784
mouse colon colorectal cancer 47 MB 4,291 obs silver H&E
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size47 MB
Obs4,291
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103781
mouse colon colorectal cancer 56 MB 4,585 obs silver H&E
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size56 MB
Obs4,585
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103780
mouse colon 42 MB 3,052 obs silver H&E
TechnologyVisium
Organismmouse
Tissuecolon
Size42 MB
Obs3,052
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM7103782
mouse colon colorectal cancer 57 MB 4,344 obs silver H&E
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolorectal cancer
Size57 MB
Obs4,344
silver H&E Open in Vitessce

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