Collections / Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer

Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer

Datasets24
Size~18.1 GB
AssayVisium
Samplehuman · kidney
KindReplicates
Flag a data issue
10.1016/j.immuni.2022.02.001 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1016-j-immuni-2022-02-001")
cohort.members        # the 24 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-10.1016/j.immuni.2022.02.001")
coll.ordered_artifacts.to_dataframe()   # the 24 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-10-1016-j-immuni-2022-02-001 --dest data/
Install (Python 3.12+) Docs →

Licenses: 24 CC BY-NC-SA 4.0

About the study

Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer.

Read the abstract at the source →
Member datasets · 24
Open in Vitessce
Visium
Human kidney
INT17
human kidney clear cell renal carcinoma 827 MB 3,585 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size827 MB
Spots3,585
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT6
human kidney clear cell renal carcinoma 539 MB 1,678 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size539 MB
Spots1,678
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT13
human kidney clear cell renal carcinoma 974 MB 4,359 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size974 MB
Spots4,359
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT22
human kidney clear cell renal carcinoma 957 MB 3,829 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size957 MB
Spots3,829
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT18
human kidney clear cell renal carcinoma 1.0 GB 4,915 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size1.0 GB
Spots4,915
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT9
human kidney clear cell renal carcinoma 504 MB 1,696 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size504 MB
Spots1,696
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT12
human kidney clear cell renal carcinoma 463 MB 1,451 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size463 MB
Spots1,451
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT24
human kidney clear cell renal carcinoma 1.2 GB 4,510 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size1.2 GB
Spots4,510
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT11
human kidney clear cell renal carcinoma 447 MB 1,439 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size447 MB
Spots1,439
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT20
human kidney clear cell renal carcinoma 980 MB 4,860 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size980 MB
Spots4,860
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT23
human kidney clear cell renal carcinoma 970 MB 4,755 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size970 MB
Spots4,755
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT4
human kidney clear cell renal carcinoma 517 MB 1,349 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size517 MB
Spots1,349
Magnification20x · 0.459 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT14
human kidney clear cell renal carcinoma 1.0 GB 4,562 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size1.0 GB
Spots4,562
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT2
human kidney clear cell renal carcinoma 590 MB 2,580 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size590 MB
Spots2,580
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT10
human kidney clear cell renal carcinoma 556 MB 1,983 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size556 MB
Spots1,983
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT15
human kidney clear cell renal carcinoma 1.1 GB 4,940 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size1.1 GB
Spots4,940
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT3
human kidney clear cell renal carcinoma 523 MB 2,007 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size523 MB
Spots2,007
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT7
human kidney clear cell renal carcinoma 621 MB 2,374 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size621 MB
Spots2,374
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT19
human kidney clear cell renal carcinoma 1.0 GB 4,948 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size1.0 GB
Spots4,948
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT8
human kidney clear cell renal carcinoma 565 MB 1,949 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size565 MB
Spots1,949
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT1
human kidney clear cell renal carcinoma 429 MB 1,084 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size429 MB
Spots1,084
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT5
human kidney clear cell renal carcinoma 477 MB 1,186 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size477 MB
Spots1,186
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT21
human kidney clear cell renal carcinoma 1.1 GB 4,975 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size1.1 GB
Spots4,975
Magnification20x · 0.457 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
INT16
human kidney clear cell renal carcinoma 723 MB 3,206 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionclear cell renal carcinoma
Size723 MB
Spots3,206
Magnification20x · 0.458 µm/px
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1016/j.immuni.2022.02.001 ↗
BibTeX 
@article{Meylan_2022,
  title = {Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer},
  volume = {55},
  ISSN = {1074-7613},
  url = {http://dx.doi.org/10.1016/j.immuni.2022.02.001},
  DOI = {10.1016/j.immuni.2022.02.001},
  number = {3},
  journal = {Immunity},
  publisher = {Elsevier BV},
  author = {Meylan, Maxime and Petitprez, Florent and Becht, Etienne and Bougoüin, Antoine and Pupier, Guilhem and Calvez, Anne and Giglioli, Ilenia and Verkarre, Virginie and Lacroix, Guillaume and Verneau, Johanna and Sun, Chen-Ming and Laurent-Puig, Pierre and Vano, Yann-Alexandre and Elaïdi, Reza and Méjean, Arnaud and Sanchez-Salas, Rafaël and Barret, Eric and Cathelineau, Xavier and Oudard, Stephane and Reynaud, Claude-Agnès and de Reyniès, Aurélien and Sautès-Fridman, Catherine and Fridman, Wolf Herman},
  year = {2022},
  month = Mar,
  pages = {527–541.e5}
}