Collections / Adult Mouse Controlled Cortical Impact Visium Spatial Transcriptomics

Adult Mouse Controlled Cortical Impact Visium Spatial Transcriptomics

Here we investigated the topographical relationship of early transcriptional responses to a single, focal TBI in mice by controlled cortical impact (CCI). Guided by the presence of the anterior commissure (AC) in coronal sections at the rostro-caudal point of impact, we compared gene expression changes in the neocortex (CTX) and corpus callosum-external capsule (CC-EC), striatum (STR) and AC. Injury-induced gene expression changes were detected in the CTX, CC-EC and STR but not AC and were principally segregated based on cytoarchitecture, and secondarily by proximity to the site of impact. Additionally, unbiased spatial clustering revealed a positive relationship between proximity to the impact and the number of acutely differentially expressed genes within the laminar CTX. Next, we examined the effects of systemic depletion of neutrophils and monocytes on spatial gene expression changes in the injured brain.

Datasets34
Size~1.8 GB
AssayVisium
Samplemouse · brain
KindTime course
Flag a data issue
PMID:41250842 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse313407")
cohort.members        # the 34 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-gse313407")
coll.ordered_artifacts.to_dataframe()   # the 34 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-gse313407 --dest data/
Install (Python 3.12+) Docs →

Licenses: 34 NCBI GEO policy

Member datasets · 34
Visium
Mouse brain
GSM9367525
mouse brain traumatic brain injury 66.8 MB 3,258 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size66.8 MB
Spots3,258
bronze H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse brain
GSM9367547
mouse brain traumatic brain injury 56.7 MB 2,717 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size56.7 MB
Spots2,717
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367532
mouse brain traumatic brain injury 47.2 MB 2,858 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size47.2 MB
Spots2,858
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367522
mouse brain traumatic brain injury 47.7 MB 2,546 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size47.7 MB
Spots2,546
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367548
mouse brain traumatic brain injury 61.7 MB 2,999 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size61.7 MB
Spots2,999
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367541
mouse brain traumatic brain injury 48.1 MB 2,459 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size48.1 MB
Spots2,459
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367529
mouse brain traumatic brain injury 43.1 MB 2,345 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size43.1 MB
Spots2,345
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367545
mouse brain traumatic brain injury 55.1 MB 2,730 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size55.1 MB
Spots2,730
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367531
mouse brain traumatic brain injury 45.6 MB 2,620 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size45.6 MB
Spots2,620
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367535
mouse brain traumatic brain injury 54.4 MB 2,749 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size54.4 MB
Spots2,749
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367544
mouse brain traumatic brain injury 52.9 MB 2,635 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size52.9 MB
Spots2,635
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367519
mouse brain traumatic brain injury 37.1 MB 1,866 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size37.1 MB
Spots1,866
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367520
mouse brain traumatic brain injury 59.1 MB 2,824 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size59.1 MB
Spots2,824
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367543
mouse brain traumatic brain injury 56.2 MB 2,750 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size56.2 MB
Spots2,750
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367534
mouse brain traumatic brain injury 40.0 MB 2,230 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size40.0 MB
Spots2,230
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367526
mouse brain traumatic brain injury 50.8 MB 2,294 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size50.8 MB
Spots2,294
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367518
mouse brain traumatic brain injury 61.5 MB 3,027 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size61.5 MB
Spots3,027
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367524
mouse brain traumatic brain injury 54.2 MB 2,724 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size54.2 MB
Spots2,724
bronze H&E NCBI GEO policy Open in Vitessce
Visium
Mouse brain
GSM9367533
mouse brain traumatic brain injury 48.9 MB 2,916 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size48.9 MB
Spots2,916
bronze H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse brain
GSM9367542
mouse brain traumatic brain injury 55.9 MB 2,706 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size55.9 MB
Spots2,706
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367521
mouse brain traumatic brain injury 60.8 MB 2,990 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size60.8 MB
Spots2,990
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367530
mouse brain traumatic brain injury 44.5 MB 2,732 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size44.5 MB
Spots2,732
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367528
mouse brain traumatic brain injury 56.0 MB 2,602 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size56.0 MB
Spots2,602
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367549
mouse brain traumatic brain injury 54.6 MB 2,844 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size54.6 MB
Spots2,844
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367550
mouse brain traumatic brain injury 47.8 MB 2,741 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size47.8 MB
Spots2,741
bronze H&E NCBI GEO policy Open in Vitessce
Visium
Mouse brain
GSM9367536
mouse brain traumatic brain injury 58.1 MB 2,499 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size58.1 MB
Spots2,499
bronze H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse brain
GSM9367538
mouse brain traumatic brain injury 53.1 MB 2,449 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size53.1 MB
Spots2,449
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367540
mouse brain traumatic brain injury 58.1 MB 2,810 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size58.1 MB
Spots2,810
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367517
mouse brain traumatic brain injury 65.9 MB 2,939 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size65.9 MB
Spots2,939
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367523
mouse brain traumatic brain injury 42.9 MB 2,288 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size42.9 MB
Spots2,288
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367537
mouse brain traumatic brain injury 62.2 MB 3,136 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size62.2 MB
Spots3,136
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM9367546
mouse brain traumatic brain injury 54.8 MB 2,660 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size54.8 MB
Spots2,660
bronze H&E NCBI GEO policy Open in Vitessce
Visium
Mouse brain
GSM9367539
mouse brain traumatic brain injury 61.7 MB 2,844 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size61.7 MB
Spots2,844
bronze H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse brain
GSM9367527
mouse brain traumatic brain injury 52.2 MB 2,514 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditiontraumatic brain injury
Size52.2 MB
Spots2,514
bronze H&E NCBI GEO policy Open in Vitessce

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