Collections / Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain

Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain

After intracranial hemorrhages, heme is released from cell-free hemoglobin. This red blood cell toxin may drive secondary brain injury at the hematoma-brain interface. This study aimed to generate a spatially resolved map of the transcriptome-wide gene expression changes in the heme-exposed brain and define the potential therapeutic activity of the heme-binding protein hemopexin.

Datasets7

Size~291 MB

AssayVisium

Samplemouse · brain

KindComparison

Flag a data issue

PMID:34793930 ↗

Download the whole collection

Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse182127")
cohort.members        # the 7 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-gse182127")
coll.ordered_artifacts.to_dataframe()   # the 7 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-gse182127 --dest data/

Install (Python 3.12+) Docs →

Licenses: 7 NCBI GEO policy

Member datasets · 7

Visium

Mouse brain

GSM5519056

mouse brain 40.9 MB 2,597 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissuebrain

Size40.9 MB

Spots2,597

Magnificationother · 3.792 µm/px

bronze H&E NCBI GEO policy

Visium

Mouse brain

GSM5519058

mouse brain 40.8 MB 2,694 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissuebrain

Size40.8 MB

Spots2,694

Magnificationother · 4.252 µm/px

bronze H&E NCBI GEO policy

Visium

Mouse brain

GSM5519054

mouse brain 39.9 MB 2,679 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissuebrain

Size39.9 MB

Spots2,679

Magnificationother · 4.229 µm/px

bronze H&E NCBI GEO policy

Visium

Mouse brain

GSM5519060

mouse brain 45.5 MB 2,780 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissuebrain

Size45.5 MB

Spots2,780

Magnificationother · 3.794 µm/px

bronze H&E NCBI GEO policy

Visium

Mouse brain

GSM5519057

mouse brain 39.4 MB 2,427 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissuebrain

Size39.4 MB

Spots2,427

Magnificationother · 4.429 µm/px

bronze H&E NCBI GEO policy

Visium

Mouse brain

GSM5519055

mouse brain 43.8 MB 2,936 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissuebrain

Size43.8 MB

Spots2,936

Magnificationother · 4.219 µm/px

bronze H&E NCBI GEO policy

Visium

Mouse brain

GSM5519059

mouse brain 40.8 MB 2,953 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismmouse

Tissuebrain

Size40.8 MB

Spots2,953

Magnificationother · 4.220 µm/px

bronze H&E NCBI GEO policy

Cite this collection

doi.org/10.1016/j.freeradbiomed.2021.11.011 ↗

BibTeX

@article{Buzzi_2022,
  title = {Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain},
  volume = {179},
  ISSN = {0891-5849},
  url = {http://dx.doi.org/10.1016/j.freeradbiomed.2021.11.011},
  DOI = {10.1016/j.freeradbiomed.2021.11.011},
  journal = {Free Radical Biology and Medicine},
  publisher = {Elsevier BV},
  author = {Buzzi, Raphael M. and Akeret, Kevin and Schwendinger, Nina and Klohs, Jan and Vallelian, Florence and Hugelshofer, Michael and Schaer, Dominik J.},
  year = {2022},
  month = Feb,
  pages = {277–287}
}