Collections / Ex-ST

Ex-ST

Datasets5
Size~5.8 GB
AssayVisium
Samplemouse · brain
KindPublication
10.1101/2022.10.25.513696 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1101/2022.10.25.513696")
coll.ordered_artifacts.df()                 # the 5 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

Expansion Spatial Transcriptomics

Capture array-based spatial transcriptomics methods have been widely used to resolve gene expression in diverse tissue contexts, however, their spatial resolution is limited by array density. We present Expansion Spatial Transcriptomics (Ex-ST) to overcome this limitation by clearing and expanding tissue prior to capturing the entire transcriptome. This approach allows us to achieve near cellular resolution and higher capture efficiency of lowly-expressed genes, which we demonstrate using mouse brain samples.

Member datasets · 5
Open in Vitessce
Visium
Mouse brain
MEND130
mouse brain 1.9 GB 4,557 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size1.9 GB
Obs4,557
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
MEND129
mouse brain 1.7 GB 4,575 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size1.7 GB
Obs4,575
Magnification40x · 0.174 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
MEND123
mouse brain 786 MB 1,490 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size786 MB
Obs1,490
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
MEND124
mouse brain 884 MB 1,448 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size884 MB
Obs1,448
Magnification40x · 0.172 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse brain
MEND131
mouse brain 504 MB 1,301 obs silver H&E
TechnologyVisium
Organismmouse
Tissuebrain
Size504 MB
Obs1,301
Magnification20x · 0.574 µm/px
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1101/2022.10.25.513696 ↗
BibTeX 
@article{Fan_2022,
  title = {Expansion Spatial Transcriptomics},
  url = {http://dx.doi.org/10.1101/2022.10.25.513696},
  DOI = {10.1101/2022.10.25.513696},
  publisher = {openRxiv},
  author = {Fan, Yuhang and Andrusivová, Žaneta and Wu, Yunming and Chai, Chew and Larsson, Ludvig and He, Mengxiao and Luo, Liqun and Lundeberg, Joakim and Wang, Bo},
  year = {2022},
  month = Oct
}