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

Datasets2
Size~511 MB
AssayVisium
Samplemouse · intestine
KindComparison
10.1016/j.crmeth.2022.100340 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1016/j.crmeth.2022.100340")
coll.ordered_artifacts.df()                 # the 2 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()}
About the study

Assessment of spatial transcriptomics for oncology discovery.

Tumor heterogeneity is a major challenge for oncology drug discovery and development. Understanding of the spatial tumor landscape is key to identifying new targets and impactful model systems. Here, we test the utility of spatial transcriptomics (ST) for oncology discovery by profiling 40 tissue sections and 80,024 capture spots across a diverse set of tissue types, sample formats, and RNA capture chemistries. We verify the accuracy and fidelity of ST by leveraging matched pathology analysis, which provides a ground truth for tissue section composition. We then use spatial data to demonstrate the capture of key tumor depth features, identifying hypoxia, necrosis, vasculature, and extracellular matrix variation. We also leverage spatial context to identify relative cell-type locations showing the anti-correlation of tumor and immune cells in syngeneic cancer models. Lastly, we demonstrate target identification approaches in clinical pancreatic adenocarcinoma samples, highlighting tumor intrinsic biomarkers and paracrine signaling.

Member datasets · 2
Open in Vitessce
Visium
Mouse intestine
NCBI728
mouse intestine ulcerative colitis 256 MB 3,630 obs silver H&E
TechnologyVisium
Organismmouse
Tissueintestine
Conditionulcerative colitis
Size256 MB
Obs3,630
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse intestine
NCBI729
mouse intestine 255 MB 2,604 obs silver H&E
TechnologyVisium
Organismmouse
Tissueintestine
Size255 MB
Obs2,604
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1016/j.crmeth.2022.100340 ↗
BibTeX 
@article{Lyubetskaya_2022,
  title = {Assessment of spatial transcriptomics for oncology discovery},
  volume = {2},
  ISSN = {2667-2375},
  url = {http://dx.doi.org/10.1016/j.crmeth.2022.100340},
  DOI = {10.1016/j.crmeth.2022.100340},
  number = {11},
  journal = {Cell Reports Methods},
  publisher = {Elsevier BV},
  author = {Lyubetskaya, Anna and Rabe, Brian and Fisher, Andrew and Lewin, Anne and Neuhaus, Isaac and Brett, Constance and Brett, Todd and Pereira, Ethel and Golhar, Ryan and Kebede, Sami and Font-Tello, Alba and Mosure, Kathy and Van Wittenberghe, Nicholas and Mavrakis, Konstantinos J. and MacIsaac, Kenzie and Chen, Benjamin J. and Drokhlyansky, Eugene},
  year = {2022},
  month = Nov,
  pages = {100340}
}