Collections / Neuroinflammatory astrocyte subtypes in the mouse brain [Visium]

Neuroinflammatory astrocyte subtypes in the mouse brain [Visium]

Spatial transcriptomics of saline- and LPS-injected Aldh1l1egfp mice 24 h after injection

Datasets6
Size~335 MB
AssayVisium
Samplemouse · brain
KindComparison
Flag a data issue
PMID:34413515 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse165098")
cohort.members        # the 6 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="geo-gse165098")
coll.ordered_artifacts.to_dataframe()   # the 6 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 geo-gse165098 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

Member datasets · 6
Open in Vitessce
Visium
Mouse brain
GSM5026148
mouse brain 54.0 MB 2,157 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size54.0 MB
Spots2,157
Magnificationother · 3.532 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM5026146
mouse brain 57.7 MB 2,728 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size57.7 MB
Spots2,728
Magnificationother · 3.531 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM5026149
mouse brain 60.9 MB 2,730 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size60.9 MB
Spots2,730
Magnificationother · 3.530 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM5026147
mouse brain 54.1 MB 2,419 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size54.1 MB
Spots2,419
Magnificationother · 3.530 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM5026144
mouse brain 55.3 MB 2,511 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size55.3 MB
Spots2,511
Magnificationother · 3.532 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM5026145
mouse brain 52.6 MB 3,113 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size52.6 MB
Spots3,113
Magnificationother · 3.531 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1038/s41593-021-00905-6 ↗
BibTeX 
@article{Hasel_2021,
  title = {Neuroinflammatory astrocyte subtypes in the mouse brain},
  volume = {24},
  ISSN = {1546-1726},
  url = {http://dx.doi.org/10.1038/s41593-021-00905-6},
  DOI = {10.1038/s41593-021-00905-6},
  number = {10},
  journal = {Nature Neuroscience},
  publisher = {Springer Science and Business Media LLC},
  author = {Hasel, Philip and Rose, Indigo V. L. and Sadick, Jessica S. and Kim, Rachel D. and Liddelow, Shane A.},
  year = {2021},
  month = Aug,
  pages = {1475–1487}
}