Lymphatic dysfunction is an integral aspect of rheumatoid arthritis (RA) pathogenesis. During "Early" arthritis in tumor necrosis factor transgenic (TNF-Tg) mice, the joint-draining popliteal lymph nodes (PLNs) dramatically expand in volume. After a prolonged expansion phase, at ~8-months-old the PLNs stochastically collapse with reduced bone volume and associated onset of "Advanced" inflammatory-erosive arthritis in affected joints. Through this pathologic process, B-cells are known to translocate into the PLN sinuses. Bulk tissue approaches (i.e. bulk genomics, flow cytometry, and ex vivo cell cultures) have been insufficient to specifically evaluate the transcriptional changes of B-cells within the sinuses of TNF-Tg PLNs. Thus, we utilized spatial transcriptomics technology to evaluate transcriptional changes in sinus B-cells and the functional genomic relationships with arthritic severity.
from sddb import Catalog
cohort = Catalog().collection("geo-gse195598")
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/")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-gse195598")
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()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse195598 --dest data/Licenses: 4 NCBI GEO policy
@article{Kenney_2023,
title = {Multi-omics analysis identifies IgG2b class-switching with ALCAM-CD6 co-stimulation in joint-draining lymph nodes during advanced inflammatory-erosive arthritis},
volume = {14},
ISSN = {1664-3224},
url = {http://dx.doi.org/10.3389/fimmu.2023.1237498},
DOI = {10.3389/fimmu.2023.1237498},
journal = {Frontiers in Immunology},
publisher = {Frontiers Media SA},
author = {Kenney, H. Mark and Rangel-Moreno, Javier and Peng, Yue and Chen, Kiana L. and Bruno, Jennifer and Embong, Abdul and Pritchett, Elizabeth and Fox, Jeffrey I. and Becerril-Villanueva, Enrique and Gamboa-Domínguez, Armando and Quataert, Sally and Muthukrishnan, Gowrishankar and Wood, Ronald W. and Korman, Benjamin D. and Anolik, Jennifer H. and Xing, Lianping and Ritchlin, Christopher T. and Schwarz, Edward M. and Wu, Chia-Lung},
year = {2023},
month = Aug
}