Collections / 10X Visium Spatial transcriptomics of murine colon in steady state and during recovery after DSS colitis

10X Visium Spatial transcriptomics of murine colon in steady state and during recovery after DSS colitis

The limitation of single-cell or bulk transcriptomic profiling is the lack of spatial topographical context. Spatial transcriptomics (ST) allows sequencing of polyadenylated transcripts from a tissue section which can be spatially mapped onto the histological brightfield image using an array of barcoded oligo-dT capturing probes. Using the 10X Visium platform, here, we unbiasedly characterized the spatial transcriptomic landscape of murine colon in steady state and during mucosal healing upon dextran sodium sulfate (DSS) induced injury

Datasets2
Size~106 MB
AssayVisium
Samplemouse · colon
KindComparison
Flag a data issue
PMID:35149721 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse169749")
cohort.members        # the 2 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-gse169749")
coll.ordered_artifacts.to_dataframe()   # the 2 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-gse169749 --dest data/
Install (Python 3.12+) Docs →

Licenses: 2 NCBI GEO policy

Member datasets · 2
Open in Vitessce
Visium
Mouse colon
GSM5213483
mouse colon 47.3 MB 2,604 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecolon
Size47.3 MB
Spots2,604
Magnificationother · 4.063 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse colon
GSM5213484
mouse colon colitis 59.1 MB 3,630 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecolon
Conditioncolitis
Size59.1 MB
Spots3,630
Magnificationother · 3.672 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1038/s41467-022-28497-0 ↗
BibTeX 
@article{Parigi_2022,
  title = {The spatial transcriptomic landscape of the healing mouse intestine following damage},
  volume = {13},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-022-28497-0},
  DOI = {10.1038/s41467-022-28497-0},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Parigi, Sara M. and Larsson, Ludvig and Das, Srustidhar and Ramirez Flores, Ricardo O. and Frede, Annika and Tripathi, Kumar P. and Diaz, Oscar E. and Selin, Katja and Morales, Rodrigo A. and Luo, Xinxin and Monasterio, Gustavo and Engblom, Camilla and Gagliani, Nicola and Saez-Rodriguez, Julio and Lundeberg, Joakim and Villablanca, Eduardo J.},
  year = {2022},
  month = Feb
}