Collections / Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC [Spatial Transcriptomics]

Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC [Spatial Transcriptomics]

Datasets2
Size~1.5 GB
AssayVisium
Samplehuman · liver
KindReplicates
Flag a data issue
10.1101/2022.11.09.515839 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1101-2022-11-09-515839")
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/")
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-10.1101/2022.11.09.515839")
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()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection doi-10-1101-2022-11-09-515839 --dest data/
Install (Python 3.12+) Docs →

Licenses: 2 CC BY-NC-SA 4.0

About the study

TREM1 <sup>+</sup> regulatory myeloid cells expand in steatohepatitis-HCC and associate with poor prognosis and therapeutic resistance to immune checkpoint blockade

Read the abstract at the source →
Member datasets · 2
Open in Vitessce
Visium
Human liver
NCBI642
human liver hepatocellular carcinoma 778 MB 1,987 spots silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionhepatocellular carcinoma
Size778 MB
Spots1,987
Magnification20x · 0.453 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human liver
NCBI643
human liver hepatocellular carcinoma 750 MB 2,261 spots silver H&E
TechnologyVisium
Organismhuman
Tissueliver
Conditionhepatocellular carcinoma
Size750 MB
Spots2,261
Magnification20x · 0.454 µm/px
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1101/2022.11.09.515839 ↗
BibTeX 
@article{Giraud_2022,
  title = {TREM1
                  <sup>+</sup>
                  regulatory myeloid cells expand in steatohepatitis-HCC and associate with poor prognosis and therapeutic resistance to immune checkpoint blockade},
  url = {http://dx.doi.org/10.1101/2022.11.09.515839},
  DOI = {10.1101/2022.11.09.515839},
  publisher = {openRxiv},
  author = {Giraud, Julie and Chalopin, Domitille and Ramel, Eloïse and Boyer, Thomas and Zouine, Atika and Derieppe, Marie-Alix and Larmonier, Nicolas and Adotevi, Olivier and Bail, Brigitte Le and Blanc, Jean-Frédéric and Chiche, Laurence and Nikolski, Macha and Saleh, Maya},
  year = {2022},
  month = Nov
}