Collections / Spatial transcriptomics reveal unnresolved wound repair as potential driver of PFA Ependymoma progression

Spatial transcriptomics reveal unnresolved wound repair as potential driver of PFA Ependymoma progression

Datasets14
Size~5.7 GB
AssayVisium
Samplehuman · brain
KindReplicates
Flag a data issue
10.1093/neuonc/noac079.165 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1093-neuonc-noac079-165")
cohort.members        # the 14 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-10.1093/neuonc/noac079.165")
coll.ordered_artifacts.to_dataframe()   # the 14 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-10-1093-neuonc-noac079-165 --dest data/
Install (Python 3.12+) Docs →

Licenses: 14 CC BY-NC-SA 4.0

Member datasets · 14
Open in Vitessce
Visium
Human brain
NCBI628
human brain ependymoma 254 MB 1,262 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size254 MB
Spots1,262
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI629
human brain ependymoma 327 MB 3,620 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size327 MB
Spots3,620
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI641
human brain ependymoma 693 MB 2,236 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size693 MB
Spots2,236
Magnification20x · 0.471 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI640
human brain ependymoma 284 MB 1,959 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size284 MB
Spots1,959
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI635
human brain ependymoma 321 MB 3,027 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size321 MB
Spots3,027
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI634
human brain ependymoma 445 MB 1,842 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size445 MB
Spots1,842
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI632
human brain ependymoma 284 MB 2,743 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size284 MB
Spots2,743
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI630
human brain ependymoma 499 MB 2,961 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size499 MB
Spots2,961
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI638
human brain ependymoma 302 MB 3,060 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size302 MB
Spots3,060
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI637
human brain ependymoma 777 MB 2,705 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size777 MB
Spots2,705
Magnification20x · 0.471 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI631
human brain ependymoma 289 MB 2,051 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size289 MB
Spots2,051
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI636
human brain ependymoma 265 MB 1,616 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size265 MB
Spots1,616
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI633
human brain ependymoma 509 MB 3,153 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size509 MB
Spots3,153
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
NCBI639
human brain ependymoma 406 MB 979 spots silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionependymoma
Size406 MB
Spots979
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1093/neuonc/noac079.165 ↗
BibTeX 
@article{Donson_2022,
  title = {EPEN-29. Spatial transcriptomic analysis of ependymoma implicates unresolved wound healing as a driver of tumor progression},
  volume = {24},
  ISSN = {1523-5866},
  url = {http://dx.doi.org/10.1093/neuonc/noac079.165},
  DOI = {10.1093/neuonc/noac079.165},
  number = {Supplement_1},
  journal = {Neuro-Oncology},
  publisher = {Oxford University Press (OUP)},
  author = {Donson, Andrew and Fu, Rui and Norris, gregory and Willard, Nicholas and Griesinger, Andrea and Riemondy, Kent and Amani, Vladimir and Grimaldo, Enrique and Harris, Faith and Hankinson, Todd and Mitra, Siddhartha and Ritzmann, timothy and Grundy, Richard and Foreman, Nicholas},
  year = {2022},
  month = June,
  pages = {i45–i45}
}