Mouse skeletal muscle tissue
NCBI646
mouse skeletal muscle tissue 510 MB 4,992 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueskeletal muscle tissue
Spots4,992
Magnification20x · 0.565 µm/px
bronze H&E
Collections / Spatial Total RNA-Sequencing of regenerating mouse hindlimb muscle and Type 1-Lang reovirus-infected mouse heart
Spatial Total RNA-Sequencing of regenerating mouse hindlimb muscle and Type 1-Lang reovirus-infected mouse heart
Datasets7
Size~3.6 GB
AssayVisium
Samplemouse · skeletal muscle tissue
KindComparison
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("doi-10-1038-s41587-022-01517-6")
cohort.members # the 7 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/") 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="doi-10.1038/s41587-022-01517-6")
coll.ordered_artifacts.to_dataframe() # the 7 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection doi-10-1038-s41587-022-01517-6 --dest data/Licenses: 7 CC BY-NC-SA 4.0
About the study
Spatial mapping of the total transcriptome by in situ polyadenylation.
Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNA enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome. We demonstrate that our spatial total RNA-sequencing (STRS) approach captures coding RNAs, noncoding RNAs and viral RNAs. We apply STRS to study skeletal muscle regeneration and viral-induced myocarditis. Our analyses reveal the spatial patterns of noncoding RNA expression with near-cellular resolution, identify spatially defined expression of noncoding transcripts in skeletal muscle regeneration and highlight host transcriptional responses associated with local viral RNA abundance. STRS requires adding only one step to the widely used Visium spatial total RNA-sequencing protocol from 10x Genomics, and thus could be easily adopted to enable new insights into spatial gene regulation and biology.
Member datasets · 7
Mouse skeletal muscle tissue
NCBI652
mouse skeletal muscle tissue 486 MB 4,992 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueskeletal muscle tissue
Spots4,992
Magnification20x · 0.562 µm/px
bronze H&E
Mouse skeletal muscle tissue
NCBI648
mouse skeletal muscle tissue 549 MB 4,992 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueskeletal muscle tissue
Spots4,992
Magnification20x · 0.563 µm/px
bronze H&E
Mouse skeletal muscle tissue
NCBI647
mouse skeletal muscle tissue 512 MB 4,992 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueskeletal muscle tissue
Spots4,992
Magnification20x · 0.564 µm/px
bronze H&E
Mouse skeletal muscle tissue
NCBI651
mouse skeletal muscle tissue 492 MB 4,992 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueskeletal muscle tissue
Spots4,992
Magnification20x · 0.562 µm/px
bronze H&E
Mouse skeletal muscle tissue
NCBI650
mouse skeletal muscle tissue 509 MB 4,992 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueskeletal muscle tissue
Spots4,992
Magnification20x · 0.563 µm/px
bronze H&E
Mouse skeletal muscle tissue
NCBI649
mouse skeletal muscle tissue 536 MB 4,992 spots bronze H&E
TechnologyVisium
Organismmouse
Tissueskeletal muscle tissue
Spots4,992
Magnification20x · 0.563 µm/px
bronze H&E
Cite this collection
doi.org/10.1038/s41587-022-01517-6 ↗ BibTeX
@article{McKellar_2022,
title = {Spatial mapping of the total transcriptome by in situ polyadenylation},
volume = {41},
ISSN = {1546-1696},
url = {http://dx.doi.org/10.1038/s41587-022-01517-6},
DOI = {10.1038/s41587-022-01517-6},
number = {4},
journal = {Nature Biotechnology},
publisher = {Springer Science and Business Media LLC},
author = {McKellar, David W. and Mantri, Madhav and Hinchman, Meleana M. and Parker, John S. L. and Sethupathy, Praveen and Cosgrove, Benjamin D. and De Vlaminck, Iwijn},
year = {2022},
month = Nov,
pages = {513–520}
}