Collections / INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease

INPP5D limits plaque formation and glial reactivity in the APP/PS1 mouse model of Alzheimer’s disease

Spatial Transcriptomics (Visium) of 12 coronal brain sections from 6 months old female Inpp5dfl/fl/Cx3cr1CreER/+ crossed to APPKM670/671NL/PSEN1Δexon9 (PSAPP) mice and treated with either cornoil or tamoxifen (75 mg/kg) at 3 months of age for 5 consecutive days

Datasets12
Size~752 MB
AssayVisium
Samplemouse · brain
KindComparison
Flag a data issue
PMID:36448627 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse203424")
cohort.members        # the 12 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-gse203424")
coll.ordered_artifacts.to_dataframe()   # the 12 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-gse203424 --dest data/
Install (Python 3.12+) Docs →

Licenses: 12 NCBI GEO policy

Member datasets · 12
Open in Vitessce
Visium
Mouse brain
GSM6171783
mouse brain 67.5 MB 3,025 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size67.5 MB
Spots3,025
Magnificationother · 3.530 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171782
mouse brain 50.4 MB 2,549 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size50.4 MB
Spots2,549
Magnificationother · 3.532 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171789
mouse brain Alzheimer disease 72.1 MB 3,078 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
ConditionAlzheimer disease
Size72.1 MB
Spots3,078
Magnificationother · 3.531 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171790
mouse brain 56.9 MB 2,647 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size56.9 MB
Spots2,647
Magnificationother · 3.534 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171787
mouse brain 74.7 MB 3,126 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size74.7 MB
Spots3,126
Magnificationother · 3.530 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Visium
Mouse brain
GSM6171793
mouse brain Alzheimer disease 54.7 MB 2,775 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
ConditionAlzheimer disease
Size54.7 MB
Spots2,775
bronze H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse brain
GSM6171788
mouse brain Alzheimer disease 65.4 MB 2,601 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
ConditionAlzheimer disease
Size65.4 MB
Spots2,601
Magnificationother · 3.533 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171791
mouse brain 57.0 MB 2,731 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size57.0 MB
Spots2,731
Magnificationother · 3.531 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171786
mouse brain 61.2 MB 2,841 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Size61.2 MB
Spots2,841
Magnificationother · 3.532 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171784
mouse brain Alzheimer disease 62.6 MB 2,731 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
ConditionAlzheimer disease
Size62.6 MB
Spots2,731
Magnificationother · 3.533 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171785
mouse brain Alzheimer disease 77.1 MB 3,513 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
ConditionAlzheimer disease
Size77.1 MB
Spots3,513
Magnificationother · 3.531 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM6171792
mouse brain Alzheimer disease 52.5 MB 2,416 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
ConditionAlzheimer disease
Size52.5 MB
Spots2,416
Magnificationother · 3.320 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1002/alz.12821 ↗
BibTeX 
@article{Castranio_2022,
  title = {Microglial
                    <i>INPP5D</i>
                    limits plaque formation and glial reactivity in the PSAPP mouse model of Alzheimer’s disease},
  volume = {19},
  ISSN = {1552-5279},
  url = {http://dx.doi.org/10.1002/alz.12821},
  DOI = {10.1002/alz.12821},
  number = {6},
  journal = {Alzheimer’s &amp; Dementia},
  publisher = {Wiley},
  author = {Castranio, Emilie L. and Hasel, Philip and Haure‐Mirande, Jean‐Vianney and Ramirez Jimenez, Angie V. and Hamilton, B. Wade and Kim, Rachel D. and Glabe, Charles G. and Wang, Minghui and Zhang, Bin and Gandy, Sam and Liddelow, Shane A. and Ehrlich, Michelle E.},
  year = {2022},
  month = Nov,
  pages = {2239–2252}
}