from sddb import Catalog
cohort = Catalog().collection("figshare-25123538")
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="figshare-25123538")
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 figshare-25123538 --dest data/Licenses: 2 CC0 1.0
Non-hematopoietic cells are essential contributors to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed co-detection by indexing (CODEX) to spatially profile over 1.2 million cells. We integrated scRNA-seq and CODEX data to link predicted cellular signaling with spatial proximity. Our analysis revealed a hyperoxygenated arterio-endosteal neighborhood for early myelopoiesis, and an adipocytic localization for early hematopoietic stem and progenitor cells (HSPCs). We used our CODEX atlas to annotate new images and uncovered mesenchymal stromal cell (MSC) expansion and spatial neighborhoods co-enriched for leukemic blasts and MSCs in acute myeloid leukemia (AML) patient samples. This spatially resolved, multiomic atlas of human bone marrow provides a reference for investigation of cellular interactions that drive hematopoiesis.
@article{Bandyopadhyay_2024,
title = {Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging},
volume = {187},
ISSN = {0092-8674},
url = {http://dx.doi.org/10.1016/j.cell.2024.04.013},
DOI = {10.1016/j.cell.2024.04.013},
number = {12},
journal = {Cell},
publisher = {Elsevier BV},
author = {Bandyopadhyay, Shovik and Duffy, Michael P. and Ahn, Kyung Jin and Sussman, Jonathan H. and Pang, Minxing and Smith, David and Duncan, Gwendolyn and Zhang, Iris and Huang, Jeffrey and Lin, Yulieh and Xiong, Barbara and Imtiaz, Tamjid and Chen, Chia-Hui and Thadi, Anusha and Chen, Changya and Xu, Jason and Reichart, Melissa and Martinez, Zachary and Diorio, Caroline and Chen, Chider and Pillai, Vinodh and Snaith, Oraine and Oldridge, Derek and Bhattacharyya, Siddharth and Maillard, Ivan and Carroll, Martin and Nelson, Charles and Qin, Ling and Tan, Kai},
year = {2024},
month = June,
pages = {3120–3140.e29}
}