Mouse eye
NCBI434
mouse eye Sjogren syndrome 238 MB 1,530 spots silver H&E
TechnologyVisium
Organismmouse
Tissueeye
ConditionSjogren syndrome
Spots1,530
silver H&E
Collections / Visium spatial transcriptomics analysis of lacrimal gland during chronic inflammation progression.
Visium spatial transcriptomics analysis of lacrimal gland during chronic inflammation progression.
Datasets4
Size~912 MB
AssayVisium
Samplemouse · eye
KindComparison
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("doi-10-3389-fimmu-2022-1011125")
cohort.members # the 4 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-10.3389/fimmu.2022.1011125")
coll.ordered_artifacts.to_dataframe() # the 4 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-10-3389-fimmu-2022-1011125 --dest data/Licenses: 4 CC BY-NC-SA 4.0
About the study
Spatial transcriptomics of the lacrimal gland features macrophage activity and epithelium metabolism as key alterations during chronic inflammation.
The lacrimal gland (LG) is an exocrine gland that produces the watery part of the tear film that lubricates the ocular surface. Chronic inflammation, such as Sjögren's syndrome (SS), is one of the leading causes of aqueous-deficiency dry eye (ADDE) disease worldwide. In this study we analyzed the chronic inflammation in the LGs of the NOD.B10Sn-H2b/J (<i>NOD.H-2b</i>) mice, a mouse model of SS, utilizing bulk RNAseq and Visium spatial gene expression. With Seurat we performed unsupervised clustering and analyzed the spatial cell distribution and gene expression changes in all cell clusters within the LG sections. Moreover, for the first time, we analyzed and validated specific pathways defined by bulk RNAseq using Visium technology to determine activation of these pathways within the LG sections. This analysis suggests that altered metabolism and the hallmarks of inflammatory responses from both epithelial and immune cells drive inflammation. The most significant pathway enriched in upregulated DEGs was the "TYROBP Causal Network", that has not been described previously in SS. We also noted a significant decrease in lipid metabolism in the LG of the <i>NOD.H-2b</i> mice. Our data suggests that modulation of these pathways can provide a therapeutic strategy to treat ADDE.
Member datasets · 4
Mouse eye
NCBI436
mouse eye 215 MB 1,135 spots silver H&E
TechnologyVisium
Organismmouse
Tissueeye
Spots1,135
silver H&E
Mouse eye
NCBI433
mouse eye Sjogren syndrome 232 MB 1,505 spots silver H&E
TechnologyVisium
Organismmouse
Tissueeye
ConditionSjogren syndrome
Spots1,505
silver H&E
Mouse eye
NCBI435
mouse eye 227 MB 1,106 spots silver H&E
TechnologyVisium
Organismmouse
Tissueeye
Spots1,106
silver H&E
Cite this collection
doi.org/10.3389/fimmu.2022.1011125 ↗ BibTeX
@article{Mauduit_2022,
title = {Spatial transcriptomics of the lacrimal gland features macrophage activity and epithelium metabolism as key alterations during chronic inflammation},
volume = {13},
ISSN = {1664-3224},
url = {http://dx.doi.org/10.3389/fimmu.2022.1011125},
DOI = {10.3389/fimmu.2022.1011125},
journal = {Frontiers in Immunology},
publisher = {Frontiers Media SA},
author = {Mauduit, Olivier and Delcroix, Vanessa and Umazume, Takeshi and de Paiva, Cintia S. and Dartt, Darlene A. and Makarenkova, Helen P.},
year = {2022},
month = Oct
}