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~203 MB
AssayVisium
Samplehuman · colon
KindComparison
Flag a data issue
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE334323 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse334323")
cohort.members        # the 6 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-gse334323")
coll.ordered_artifacts.to_dataframe()   # the 6 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-gse334323 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

Member datasets · 6
Open in Vitessce
Visium
Human colon
GSM9785428
human colon 12.4 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecolon
Size12.4 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785433
human colon colorectal carcinoma 51.7 MB 4,898 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecolon
Conditioncolorectal carcinoma
Size51.7 MB
Spots4,898
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785431
human colon colorectal carcinoma 41.6 MB 3,909 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecolon
Conditioncolorectal carcinoma
Size41.6 MB
Spots3,909
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785429
human colon colorectal carcinoma 18.2 MB 4,682 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecolon
Conditioncolorectal carcinoma
Size18.2 MB
Spots4,682
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human colon
GSM9785430
human colon 47.7 MB 3,689 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecolon
Size47.7 MB
Spots3,689
silver H&E NCBI GEO policy Open in Vitessce
Visium
Human colon
GSM9785432
human colon 31.8 MB 3,565 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuecolon
Size31.8 MB
Spots3,565
silver H&E NCBI GEO policy

Cite this collection

No linked publication found — please cite the data source.