We performed Spatial transcriptomics (Visium) using the 10X Genomics platform to investigate the role of the autophagy-related protein ATG7 in the context of nontuberculous mycobacterial (NTM) infection. ATG7 in innate immune cells plays a critical role in controlling NTM infection and protecting lung tissue from pathological inflammation. This study represents single-cell analysis of Mice deletion of Atg7 in innate immune cells and reveals the importance of ATG7 in mediating antimicrobial responses during infection and its essential role in host defense mechanisms against NTM.
from sddb import Catalog
cohort = Catalog().collection("geo-gse297621")
cohort.members # the 2 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-gse297621")
coll.ordered_artifacts.to_dataframe() # the 2 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-gse297621 --dest data/Licenses: 2 NCBI GEO policy
@article{Jeon_2025,
title = {ATG7 in innate immune cells is required for host defense against nontuberculous mycobacterial pulmonary infections},
volume = {16},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-025-61791-1},
DOI = {10.1038/s41467-025-61791-1},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Jeon, Sang Min and Lee, Yeon Ju and Lee, Sang-Hee and Kim, Soo In and Lee, Bomi and Roh, Taylor and Kim, Young Jae and Kim, Hyeon Ji and Kim, In Soo and Whang, Jake and Kim, So-young and Jhun, Byung Woo and Chung, Chaeuk and Kang, Da Hyun and Yeo, Min-Kyung and Kim, Jin-Man and Jang, Jichan and Min, Jung-Joon and Komatsu, Masaaki and Kim, Jin Kyung and Park, Woong-Yang and Jo, Eun-Kyeong},
year = {2025},
month = July
}