Collections / A cellular hierarchy in melanoma uncouples growth and metastasis

A cellular hierarchy in melanoma uncouples growth and metastasis

Datasets3
Size~706 MB
AssayVisium
Samplemouse · skin of body
KindPublication
Flag a data issue
10.1038/s41586-022-05242-7 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1038-s41586-022-05242-7")
cohort.members        # the 3 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/")
Install (Python 3.12+) Docs →
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/s41586-022-05242-7")
coll.ordered_artifacts.to_dataframe()   # the 3 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection doi-10-1038-s41586-022-05242-7 --dest data/
Install (Python 3.12+) Docs →

Licenses: 3 CC BY-NC-SA 4.0

About the study

A cellular hierarchy in melanoma uncouples growth and metastasis.

Read the abstract at the source →
Member datasets · 3
Open in Vitessce
Visium
Mouse skin of body
NCBI689
mouse skin of body cutaneous melanoma 240 MB 4,992 spots silver H&E
TechnologyVisium
Organismmouse
Tissueskin of body
Conditioncutaneous melanoma
Size240 MB
Spots4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse skin of body
NCBI687
mouse skin of body cutaneous melanoma 244 MB 4,992 spots silver H&E
TechnologyVisium
Organismmouse
Tissueskin of body
Conditioncutaneous melanoma
Size244 MB
Spots4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse skin of body
NCBI688
mouse skin of body cutaneous melanoma 222 MB 4,992 spots silver H&E
TechnologyVisium
Organismmouse
Tissueskin of body
Conditioncutaneous melanoma
Size222 MB
Spots4,992
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1038/s41586-022-05242-7 ↗
BibTeX 
@article{Karras_2022,
  title = {A cellular hierarchy in melanoma uncouples growth and metastasis},
  volume = {610},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-022-05242-7},
  DOI = {10.1038/s41586-022-05242-7},
  number = {7930},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Karras, Panagiotis and Bordeu, Ignacio and Pozniak, Joanna and Nowosad, Ada and Pazzi, Cecilia and Van Raemdonck, Nina and Landeloos, Ewout and Van Herck, Yannick and Pedri, Dennis and Bervoets, Greet and Makhzami, Samira and Khoo, Jia Hui and Pavie, Benjamin and Lamote, Jochen and Marin-Bejar, Oskar and Dewaele, Michael and Liang, Han and Zhang, Xingju and Hua, Yichao and Wouters, Jasper and Browaeys, Robin and Bergers, Gabriele and Saeys, Yvan and Bosisio, Francesca and van den Oord, Joost and Lambrechts, Diether and Rustgi, Anil K. and Bechter, Oliver and Blanpain, Cedric and Simons, Benjamin D. and Rambow, Florian and Marine, Jean-Christophe},
  year = {2022},
  month = Sept,
  pages = {190–198}
}