Collections / Visium Spatial transcriptomics analysis of human primary colorectal cancer

Visium Spatial transcriptomics analysis of human primary colorectal cancer

To reveal the spatial distribution and the difference gene expression pattern of cancer cells in colorectal cancer, Visium spatial transcriptomics of four CRC patients was applied

Datasets4
Size~229 MB
AssayVisium
Samplehuman · colorectum
KindReplicates
PMID:38446659 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse226997")
coll.ordered_artifacts.df()                 # the 4 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()}
Open in Vitessce
Visium
Human colorectum
GSM7089857
human colorectum colorectal cancer 67 MB 4,676 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolorectum
Conditioncolorectal cancer
Size67 MB
Obs4,676
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human colorectum
GSM7089858
human colorectum colorectal cancer 36 MB 3,535 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolorectum
Conditioncolorectal cancer
Size36 MB
Obs3,535
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human colorectum
GSM7089856
human colorectum colorectal cancer 51 MB 3,737 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolorectum
Conditioncolorectal cancer
Size51 MB
Obs3,737
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human colorectum
GSM7089855
human colorectum colorectal cancer 76 MB 4,148 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolorectum
Conditioncolorectal cancer
Size76 MB
Obs4,148
silver H&E Open in Vitessce

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