Collections / Custom Probe-Based Spatial Transcriptomics Enables Microbiome Detection in FFPE Colorectal Cancer Tissue

Custom Probe-Based Spatial Transcriptomics Enables Microbiome Detection in FFPE Colorectal Cancer Tissue

We describe a custom probe design pipeline targeting the variable regions of bacterial 16S rRNA, compatible with the probe-based chemistry of the 10X Genomics Visium CytAssist platform, enabling spatially resolved bacterial profiling in FFPE tissue. Applied to a cohort of six FFPE colorectal cancer tumor and normal adjacent tissue specimens, we demonstrate the feasibility of a probe-based spatial metatranscriptomics for simultanous profiling of host gene expression and the intratumoral bacterial communities.

Datasets6
Size~194 MB
AssayVisium
Samplehuman · colon
KindComparison
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE334323 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse334323")
coll.ordered_artifacts.df()                 # the 6 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 · 6
Open in Vitessce
Visium
Human colon
GSM9785428
human colon 12 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolon
Size12 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785433
human colon colorectal carcinoma 49 MB 4,898 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolon
Conditioncolorectal carcinoma
Size49 MB
Obs4,898
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785431
human colon colorectal carcinoma 40 MB 3,909 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolon
Conditioncolorectal carcinoma
Size40 MB
Obs3,909
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785429
human colon colorectal carcinoma 17 MB 4,682 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolon
Conditioncolorectal carcinoma
Size17 MB
Obs4,682
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785430
human colon 45 MB 3,689 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolon
Size45 MB
Obs3,689
silver H&E Open in Vitessce
Visium
Human colon
GSM9785432
human colon 30 MB 3,565 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecolon
Size30 MB
Obs3,565
silver H&E

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